US20040185504A1 - Microplate thermal shift assay apparatus for ligand development and multi-variable protein chemistry optimization - Google Patents

Microplate thermal shift assay apparatus for ligand development and multi-variable protein chemistry optimization Download PDF

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US20040185504A1
US20040185504A1 US10/821,274 US82127404A US2004185504A1 US 20040185504 A1 US20040185504 A1 US 20040185504A1 US 82127404 A US82127404 A US 82127404A US 2004185504 A1 US2004185504 A1 US 2004185504A1
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samples
temperature
protein
heat conducting
assay
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Michael Pantoliano
Roger Bone
Alexander Rhind
Francis Salemme
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Janssen Research and Development LLC
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Johnson and Johnson Pharmaceutical Research and Development LLC
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B30/00—Methods of screening libraries
    • C40B30/04—Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L7/00—Heating or cooling apparatus; Heat insulating devices
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L7/00—Heating or cooling apparatus; Heat insulating devices
    • B01L7/52—Heating or cooling apparatus; Heat insulating devices with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C07K1/04—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers
    • C07K1/047—Simultaneous synthesis of different peptide species; Peptide libraries
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6811—Selection methods for production or design of target specific oligonucleotides or binding molecules
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
    • G01N33/6845—Methods of identifying protein-protein interactions in protein mixtures
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/86—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving blood coagulating time or factors, or their receptors
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N35/02—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations
    • G01N35/028—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations having reaction cells in the form of microtitration plates
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Definitions

  • the present invention relates generally to the screening of compound and combinatorial libraries. More particularly, the present invention relates to a method and apparatus for performing assays, particularly thermal shift assays.
  • a combinatorial library is a collection of chemical compounds which have been generated, by either chemical synthesis or biological synthesis, by combining a number of chemical “building blocks” as reagents.
  • a combinatorial polypeptide library is formed by combining a set of amino acids in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide compound). Millions of chemical compounds can theoretically be synthesized through such combinatorial mixing of chemical building blocks. Indeed, one investigator has observed that the systematic, combinatorial mixing synthesis of 100 million tetrameric compounds or 10 billion pentameric compounds (Gordon, E. M. et al., J. Med. Chem . 37:1233-1251 (1994)).
  • DirectedDiversity® is a computer based, iterative process for generating chemical entities with defined physical, chemical and/or bioactive properties.
  • the DirectedDiversitye system is disclosed in U.S. Pat. No. 5,463,564, which is herein incorporated by reference in its entirety.
  • each compound in the library is equilibrated with a target molecule of interest, such as an enzyme.
  • a target molecule of interest such as an enzyme.
  • a variety of approaches have been used to screen combinatorial libraries for lead compounds. For example, in an encoded library, each compound in a chemical combinatorial library can be made so that an oligonucleotide “tag” is linked to it. A careful record is kept of the nucleic acid tag sequence for each compound. A compound which exerts an effect on the target enzyme is selected by amplifying its nucleic acid tag using the polymerase chain reaction (PCR).
  • PCR polymerase chain reaction
  • a filamentous phage display peptide library can be screened for binding to a biotinylated antibody, receptor or other binding protein.
  • the bound phage is used to infect bacterial cells and the displayed determinant (i.e., the peptide ligand) is then identified (Scott, J. K. et al., Science 249:386-390 (1990)).
  • This approach suffers from several drawbacks. It is time consuming. Peptides which are toxic to the phage or to the bacterium cannot be studied. Moreover, the researcher is limited to investigating peptide compounds.
  • a challenge presented by currently available combinatorial library screening technologies is that they provide no information about the relative binding affinities of different ligands for a receptor protein. This is true whether the process for generating a combinatorial library involves phage library display of peptides (Scott, J. K. et al., Science 249:386-390 (1990)), random synthetic peptide arrays (Lam, K. S. et al., Nature 354:82-84 (1991)), encoded chemical libraries (Brenner, S. et al., Proc. Natl. Acad. Sci. USA 89:5381-5383 (1992)), the method of Hudson (Intl. Appl. WO 94/05394), or most recently, combinatorial organic synthesis (Gordon, E. et al., J. Med Chem . 37:1385-1399 (1994)).
  • a given assay is not applicable to more than one receptor. That is, when a new receptor becomes available for testing, a new assay must be developed. For many receptors, reliable assays are simply not available. Even if an assay does exist, it may not lend itself to automation. Further, if a K i is the endpoint to be measured in a kinetic assay, one must first guess at the concentration of inhibitor to use, perform the assay, and then perform additional assays using at least six different concentrations of inhibitor. If one guesses too low, an inhibitor will not exert its inhibitory effect at the suboptimal concentration tested.
  • Thermal protein unfolding, or thermal “shift,” assays have been used to determine whether a given ligand binds to a target receptor protein.
  • a change in a biophysical parameter of a protein is monitored as a function of increasing temperature.
  • the physical parameter measured is the change in heat capacity as a protein undergoes temperature induced unfolding transitions.
  • Differential scanning calorimetry has been used to measure the affinity of a panel of azobenzene ligands for streptavidin (Weber, P. et al., J. Am. Chem. Soc . 16:2717-2724 (1994)).
  • the recombinant protein When bacterial cells are used to overexpress exogenous proteins, the recombinant protein is often sequestered in bacterial cell inclusion bodies. For the recombinant protein to be useful, it must be purified from the inclusion bodies. During the purification process, the recombinant protein is denatured and must then be renatured. It is impossible to predict the renaturation conditions that will facilitate and optimize proper refolding of a given recombinant protein. Usually, a number of renaturing conditions must be tried before a satisfactory set of conditions is discovered.
  • thermal shift assays have not been performed that way. Instead, the conventional approach to performing thermal shift assays has been to heat and assay only one sample at a time. That is, researchers conventionally 1) heat a sample to a desired temperature in a heating apparatus; 2) assay a physical change, such as absorption of light or change in secondary, tertiary, or quaternary protein structure; 3) heat the samples to the next highest desired temperature; 4) assay for a physical change; and 5) continue this process repeatedly until the sample has been assayed at the highest desired temperature.
  • the present invention provides a multi-variable method for ranking the efficacy of one or more of a multiplicity of different molecules or different biochemical conditions for stabilizing a target molecule which is capable of denaturing due to a thermal change.
  • the method comprises contacting the target molecule with one or more of a multiplicity of different molecules or different biochemical conditions in each of a multiplicity of containers, simultaneously heating the multiplicity of containers, measuring in each of the containers a physical change associated with the thermal denaturation of the target molecule resulting from heating, generating a thermal denaturation curve for the target molecule as a function of temperature for each of the containers, comparing each of the denaturation curves to (i) each of the other thermal denaturation curves and to (ii) the thermal denaturation curve obtained for the target molecule under a reference set of biochemical conditions, and ranking the efficacies of multiplicity of different molecules or the different biochemical conditions according to the change in each of the thermal denaturation curves.
  • the present invention provides a multi-variable method for optimizing the shelf life of a target molecule which is capable of denaturing due to a thermal change.
  • the method comprises contacting the target molecule with one or more of a multiplicity of different molecules or different biochemical conditions in each of a multiplicity of containers, simultaneously heating the multiplicity of containers, measuring in each of the containers a physical change associated with the thermal denaturation of the target molecule resulting from heating, generating a thermal denaturation curve for the target molecule as a function of temperature for each of the containers, comparing each of the denaturation curves to (i) each of the other thermal denaturation curves and to (ii) the thermal denaturation curve obtained for the target under a reference set of biochemical conditions, and ranking the efficacies of multiplicity of different molecules or the different biochemical conditions according to the change in each of the thermal denaturation curves.
  • the present invention also provides a multi-variable method for ranking the affinity of a combination of two or more of a multiplicity of different molecules for a target molecule which is capable of denaturing due to a thermal change.
  • the method comprises contacting the target molecule with a combination of two or more different molecules of the multiplicity of different molecules in each of a multiplicity of containers, simultaneously heating the multiplicity of containers, measuring in each of the containers a physical change associated with the thermal denaturation of the target molecule resulting from the heating, generating a thermal denaturation curve for the target molecule as a function of temperature for each of the containers, comparing each of the thermal denaturation curves with (i) each of the other thermal denaturation curves obtained for the target molecule and to (ii) the thermal denaturation curve for the target molecule in the absence of any of the two or more different molecules, and ranking the affinities of the combinations of the two or more multiplicity of different molecules according to the change in each of the thermal denaturation curves.
  • the present invention also provides a multi-variable method for ranking the efficacies of one or more of a multiplicity of different biochemical conditions to facilitate the refolding of a sample of a denatured protein.
  • the method comprises placing one of the refolded protein samples in each of a multiplicity of containers, wherein each of the refolded protein samples has been previously refolded according to one or more of the multiplicity of conditions, simultaneously heating the multiplicity of containers, measuring in each of the containers a physical change associated with the thermal denaturation of the protein resulting from heating, generating a thermal denaturation curve for the protein as a function of temperature for each of the containers, comparing each of the denaturation curves to (i) each of the other thermal denaturation curves and to (ii) the thermal denaturation curve obtained for the native protein under a reference set of biochemical conditions, and ranking the efficacies of the multiplicity of different refolding conditions according to the change in the magnitude of the physical change of each of the thermal den
  • the present invention also provides a further multi-variable method for ranking the efficacies of one or more of a multiplicity of different biochemical conditions to facilitate the refolding of a sample of a denatured protein, which comprises determining one or more combinations of a multiplicity of different conditions which promote protein stabililty, folding the denatured protein under said one or more combinations of biochemical conditions that were identified as promoting protein stabilization, asseessing folded protein yield, ranking the efficacies of said multiplicity of different refolding conditions according to folded protein yield, and repeating these steps until a combination of biochemical conditions that promote optimal protein folding are identified.
  • biochemical conditions have an additive effect on protein stability. Once a set of biochemical conditions that facilitate an increase in protein stability have been identified using the thermal shift assay, the same set of conditions can be used in protein folding experiments with recombinant protein. If the conditions that promote protein stability in the thermal shift assay correlate with conditions that promote folding of recombinant protein, conditions can be further optimized by performing additional thermal shift assays until a combination of stabilizing conditions that result in further increase protein stability are identified. Recombinant protein is then folded under those conditions. This process is repeated until optimal folding conditions are identified.
  • the present invention also provides a multi-variable method for ranking the efficacy of one or more of a multiplicity of different biochemical conditions for facilitating the crystallization of a protein which is capable of denaturing due to a thermal change.
  • the method comprises contacting the protein with one or more of the multiplicity of different biochemical conditions in each of a multiplicity of containers, simultaneously heating the multiplicity of containers, measuring in each of the containers a physical change associated with the thermal denaturation of the protein resulting from the heating, generating a thermal denaturation curve for the protein as a function of temperature for each of the containers, comparing each of the denaturation curves to (i) each of the other thermal denaturation curves and (ii) to the thermal denaturation curve obtained using a reference set of biochemical conditions, and ranking the efficacies of the multiplicity of different biochemical conditions according to the change in each of the thermal denaturation curves.
  • the present invention also provides a method for ranking the affinity of each of a multiplicity of different molecules for a target molecule which is capable of denaturing due to a thermal change.
  • the method comprises contacting the target molecule with one molecule of a multiplicity of different molecules in each of a multiplicity of containers, simultaneously heating the containers, measuring in each of the containers a physical change associated with the thermal denaturation of the target molecule resulting from heating, generating a thermal denaturation curve for the target molecule as a function of temperature in each of the containers, comparing each of the thermal denaturation curves with the thermal denaturation curve obtained for the target molecule in the absence of any of the molecules in the multiplicity of different molecules, and ranking the affinities of each molecule according to the change in each of the thermal denaturation curves.
  • the present invention also provides a method for assaying a pool or collection of a multiplicity of different molecules for a molecule which binds to a target molecule which is capable of denaturing due to a thermal change.
  • the method comprises contacting the target molecule with a collection of at least two molecules of a multiplicity of different molecules in each of a multiplicity of containers, simultaneously heating the multiplicity of containers, measuring in each of the containers a physical change associated with the thermal denaturation of the target molecule resulting from heating, generating a set of thermal denaturation curves for the target molecule as a function of temperature for each of the containers, comparing each of the thermal denaturation curves with the thermal denaturation curve obtained for the target molecule in the absence of any of the molecules in the multiplicity of different molecules, ranking the affinities of the collections of different molecules according to the change in each of the thermal denaturation curves, selecting the collection of different molecules which contains a molecule with affinity for the target molecule, dividing the selected collection into smaller collections of molecules in
  • This invention also provides an improved method for generating lead compounds which comprises synthesizing a multiplicity of compounds and testing the ability of each compound to bind to a receptor molecule.
  • the improvement comprises contacting the receptor molecule with one compound of a multiplicity of different compounds in each of a multiplicity of wells in a microplate, simultaneously heating the wells, measuring in each of the wells a physical change, resulting from heating, associated with the thermal denaturation of the receptor molecule, generating a thermal denaturation curve for the receptor molecule as a function of temperature in each of the wells, comparing each of the thermal denaturation curves with the thermal denaturation curve obtained for the receptor molecule in the absence of any of the compounds in the multiplicity of different compounds, and ranking the affinities of each compound according to the change in each of the thermal denaturation curves.
  • the present invention also provides a product of manufacture which comprises a carrier having a multiplicity of containers therein, each of the containers containing a target molecule which is capable of denaturation due to heating, and at least one molecule selected from a multiplicity of different molecules present in a combinatorial library, wherein each of the different molecules are present in a different one of the multiplicity of containers in the carrier.
  • Multi-variable optimization problems require large numbers of parallel experiments to collect as much data as possible in order to determine which variables influence a favorable response.
  • multi-variable optimization problems require large numbers of parallel experiments to collect as much data as possible in order to determine which variables influence protein stabililty.
  • both protein crystallization and quantitative structure activity relationship analyses have greatly benefited from mass screening protocols that employ matrix arrays of incremental changes in biochemical or chemical composition.
  • the methods and apparatus of the present invention facilitate the construction of a quantitative model that relates different biochemical conditions to experimentally measured protein stability, ligand specificity, folded protein yield, and crystallized protein yield.
  • the present invention offers a number of advantages over previous technologies that are employed to optimize multi-variable events such as protein stabilization, ligand binding, protein folding, and protein crystallization. Foremost among these advantages is that the present invention facilitates high throughput screening. Further, the present invention offers a number of advantages over previous technologies that are employed to screen combinatorial libraries. Foremost among these advantages is that the present invention facilitates high throughput screening of combinatorial libraries for lead compounds. Many current library screening technologies simply indicate whether a ligand binds to a receptor or not. In that case, no quantitative information is provided. No information about the relative binding affinities of a series of ligands is provided.
  • the present invention facilitates the ranking of a series of compounds for their relative affinities for a target receptor.
  • a structure-activity relationship can be developed for a set of compounds.
  • T m midpoint unfolding temperature
  • the conventional kinetic screening approach requires at least six additional well assays at six different concentrations of inhibitor to determine a K i .
  • throughput is enhanced ⁇ 6 fold over the enzyme based assays because one complete binding experiment can be performed in each well of a multiwell microplate.
  • the kinetic screening approached are even further limited by the usual compromise between dilution and signal detection, which usually occurs at a protein concentration of about 1 nM.
  • the calorimetric approaches either differential scanning calorimetry or isothermal titrating calorimetry, are at an even worse disadvantage since they are limited to solitary binding experiments, usually 1 per hour.
  • the present invention affords a wide dynamic range of measurable binding affinities, from ⁇ 10 ⁇ 4 to 10 ⁇ 15 M, in a single well.
  • the present invention does not require radioactively labeled compounds. Nor does it require that receptors be labeled with a fluorescent or chromophoric label.
  • a very important advantage of the present invention is that it can be applied universally to any receptor that is a drug target Thus, it is not necessary to invent a new assay every time a new receptor becomes available for testing.
  • the receptor under study is an enzyme
  • researchers can determine the rank order of affinity of a series of compounds more quickly and more easily than they can using conventional kinetic methods.
  • researchers can detect ligand binding to an enzyme, regardless of whether binding occurs at the active site, at an allosteric cofactor binding site, or at a receptor subunit interface.
  • the present invention is equally applicable to non-enzyme receptors, such as proteins and nucleic acids.
  • an assay apparatus in a further aspect of the present invention, includes a heating means for simultaneously heating a plurality of samples, and a receiving means for receiving spectral emission from the samples while the samples are being heated.
  • an assay apparatus in yet a further aspect of the present invention, includes a temperature adjusting means for simultaneously adjusting a temperature of a plurality of samples in accordance with a pre-determined temperature profile, and a receiving means for receiving spectral emission from the samples while the temperature of the samples is adjusted in accordance with the temperature profile.
  • the present invention also provides an assay apparatus that includes a movable platform on which are disposed a plurality of heat conducting blocks.
  • the temperature of the heat conducting blocks, and their samples, are adjusted by a temperature adjusting means.
  • Each of the plurality of heat conducting blocks is adapted to receive a plurality of samples.
  • a light source is provided for emitting an excitatory wavelength of light for the samples. While the temperature of the samples is being adjusted, a sensor detects the spectral emission from the samples in response to the excitatory wavelength of light.
  • the movable platform is moved between heat conducting blocks to sequentially detect spectral emission from the samples in each of the plurality of heat conducting blocks.
  • the assay apparatus of the present invention affords the artisan the opportunity to rapidly screen molecules and biochemical conditions that affect protein stability. Samples are simultaneously heated over a range of temperatures. During heating, spectral emissions are received.
  • the assay apparatus of the present invention also provides the artisan with an opportunity for conveniently and efficiently carrying out the methods of the present invention.
  • the assay apparatus of the present invention is particularly adapted for carrying out thermal shift assays of molecules and biochemical conditions that stabilize target proteins.
  • the apparatus of the present invention comprises both a heating means and a spectral emission receiving means
  • the apparatus of the present invention obviates the need to heat samples in one apparatus and transfer the samples to another apparatus prior to taking spectral emission readings.
  • the apparatus of the present invention facilitates changing temperature in accordance with a pre-determined temperature profile, rather than incremental temperature increases and intermediate cooling steps. Thus, more data points can be collected for a given sample and more accurate information can be obtained.
  • the assay apparatus of the present invention comprises both a heating means and a spectral emission receiving means, spectral measurements can be taken from the samples while they are being heated.
  • the artisan can study both irreversibly unfolding proteins and reversibly folding proteins.
  • FIG. 1 shows the results of a microplate thermal shift assay for ligands which bind to the active site of human ⁇ -thrombin (with turbidity as the experimental signal).
  • FIG. 2 shows the results of a microplate thermal shift assay for ligands which bind to acidic fibroblast growth factor (aFGF) (with turbidity as the experimental signal).
  • aFGF acidic fibroblast growth factor
  • FIG. 3 shows the results of a microplate thermal shift assay for ligand binding to the active site of human ⁇ -thrombin (with fluorescence emission as the experimental signal).
  • the lines drawn through the data points represent non-linear least squares curve fits of the data using the equation shown at the bottom of the figure. There are five fitting parameters for this equation of y(T) vs.
  • T (1) y f , the pre-transitional fluorescence for the native protein; (2) y u , the post-transitional fluorescence for the unfolded protein; (3) T m , the temperature at the midpoint for the unfolding transition; (4) ⁇ H u , the van't Hoff unfolding enthalpy change; and (5) ⁇ C pu , the change in heat capacity upon protein unfolding.
  • the non-linear least squares curve fitting was accomplished using KaleidaGraphTM 3.0 software (Synergy Software, Reading Pa.), which allows the five fitting parameters to float while utilizing Marquardt methods for the minimization of the sum of the squared residuals.
  • FIG. 4 shows the result of a microplate thermal shift assay of ligands which bind to the D(II) domain of human FGF receptor 1 (D(II) FGFR1) (with fluorescence emission as the experimental signal).
  • the lines drawn through the data points represent non-linear least squares curve fits of the data using the equation shown at the bottom of the figure, as described for FIG. 3.
  • FIG. 5 shows the results of a miniaturized microplate thermal shift assay for Factor D in the absence of any ligands.
  • FIG. 6 shows the results of a microplate thermal shift assay for Factor Xa in the absence of any ligands.
  • FIG. 7 shows the results of a miniaturized microplate thermal shift assay of a ligand that binds to the catalytic site of human ⁇ -thrombin.
  • FIG. 8 shows the results of a miniaturized microplate thermal shift assay of aprosulate binding to the D(II) domain of human FGF receptor 1.
  • FIG. 9 shows the results of a miniaturized microplate thermal shift assay for urokinase in the presence of glu-gly-arg chloromethylketone.
  • FIG. 10 shows the results of a miniaturized microplate thermal shift assay of human ⁇ -thrombin in which the assay volume is 2 ⁇ l. Thermal denaturation curves for three experiments are shown.
  • FIG. 11 shows the results of a miniaturized microplate thermal shift assay of human ⁇ -thrombin in which the assay volume is 5 ⁇ l. Thermal denaturation curves for five experiments are shown.
  • FIG. 12 shows the results of a single temperature microplate thermal shift assay of human ⁇ -thrombin in the presence of four different compounds in four separate experiments.
  • FIG. 13 shows the results of a microplate thermal shift assay of the intrinsic tryptophan fluorescence of human ⁇ -thrombin. In this assay, blank well fluorescence was not subtracted from sample fluorescence.
  • FIG. 14 shows the results of a microplate thermal shift assay of the intrinsic tryptophan fluorescence of human ⁇ -thrombin. In this assay, blank well fluorescence was subtracted from sample fluorescence.
  • FIG. 15 shows the results of microplate thermal shift assays of single ligand binding interactions to three different classes of binding sites for human ⁇ -thrombin.
  • FIG. 16 shows the results of microplate thermal shift assays of multi-ligand binding interactions for human ⁇ -thrombin.
  • FIGS. 17 A-D show the results of microplate thermal shift assays of the effect of pH and various sodium chloride concentrations on the stability of human ⁇ -thrombin.
  • the fluorophore is 1,8-ANS.
  • the fluorophore is 2,6-ANS.
  • the fluorophore is 2,6-TNS.
  • the fluorophore is bis-ANS.
  • FIG. 18 shows the results of microplate thermal shift assays of the effect of calcium chloride, ethylenediaminetetraacetic acid, dithiothreitol, and glycerol on the stability of human ⁇ -thrombin.
  • FIG. 19 shows the results of microplate thermal shift assays of the effect of pH and sodium chloride concentration of the stability of human D(II) FGF receptor 1.
  • FIG. 20 shows the results of microplate thermal shift assays of the effect of various biochemical conditions on the stability of human D(II) FGF receptor 1.
  • FIG. 21 shows the results of microplate thermal shift assays of the effect of various biochemical conditions on the stability of human D(II) FGF receptor 1.
  • FIG. 22 shows the results of microplate thermal shift assays of the effect of various biochemical conditions on the stability of human D(II) FGF receptor 1.
  • FIG. 23 shows the results of microplate thermal shift assays of the effect of various biochemical conditions on the stability of human D(II) FGF receptor 1.
  • FIG. 24 shows the results of microplate thermal shift assays of the effect of various biochemical conditions on the stability of human D(II) FGF receptor 1.
  • FIG. 25 shows the results of microplate thermal shift assays of the effect of various biochemical conditions on the stability of human urokinase.
  • FIG. 26 is a schematic diagram of a thermodynamic model for the linkage of the free energies of protein folding and ligand binding.
  • FIG. 27 is a schematic diagram of a method of screening biochemical conditions that optimize protein folding.
  • FIG. 28 shows the results of microplate thermal shift assays of human ⁇ -thrombin stability using various fluorophores.
  • FIG. 29 shows a schematic diagram of one embodiment of an assay apparatus of the present invention.
  • FIG. 30 shows a schematic diagram of an alternate embodiment of the assay apparatus of the present invention.
  • FIG. 31 shows a schematic diagram of the assay apparatus according to another embodiment of the present invention.
  • FIGS. 32 A-E illustrate one embodiment of a thermal electric stage for the assay apparatus of the present invention.
  • FIG. 32A shows a side view of the thermal electric stage.
  • FIG. 32B shows a top view of the thermal electric stage.
  • FIGS. 32 C-E show three configurations of inserts that can be attached to the thermal electric stage.
  • inserts accommodate a microtitre plate.
  • assay samples are contained within the wells of the microtitre plate.
  • FIG. 33 is a schematic diagram illustrating a top view of another embodiment of the assay apparatus of the present invention.
  • FIG. 34 is a schematic diagram illustrating the top view of the embodiment of the assay apparatus shown in FIG. 33 with a housing installed.
  • FIG. 35 is a schematic diagram illustrating a side view of the embodiment of the assay apparatus shown in FIGS. 33 and 34.
  • FIGS. 36A and 36B illustrate a temperature profile and how the temperature profile is implemented using the automated assay apparatus of the present invention.
  • FIG. 37 shows an exemplary computer system suitable for use with the present invention.
  • FIG. 38 shows a flow diagram illustrating one embodiment for implementation of the present invention.
  • FIG. 39 shows a flow diagram illustrating an alternate embodiment for implementation of the present invention.
  • FIG. 40 shows a comparison of the results of microplate thermal shift assays of human ⁇ -thrombin denaturation performed using a fluorescence scanner and a CCD camera.
  • FIGS. 41A and 41B show photographs of microplate thermal shift assay of human ⁇ -thrombin denaturation performed using a CCD camera.
  • FIG. 41A V-bottom well microplate.
  • FIG. 41B dimple microplate.
  • FIG. 42 shows a comparison of the results of microplate thermal shift assays of human ⁇ -thrombin denaturation performed using a fluorescence scanner and a CCD camera.
  • the present invention provides a method for ranking a multiplicity of different molecules in the order of their ability to bind to a target molecule which is capable of unfolding due to a thermal change.
  • the target molecule is contacted with one molecule of a multiplicity of different molecules in each of a multiplicity of containers.
  • the containers are then simultaneously heated, in intervals, over a range of temperatures. After each heating interval, a physical change associated with the thermal denaturation of the target molecule is measured.
  • the containers are heated in a continuous fashion. A thermal denaturation curve is plotted as a function of temperature for the target molecule in each of the containers.
  • the temperature midpoint, T m of each thermal denaturation curve is identified and is then compared to the T m of the thermal denaturation curve obtained for the target molecule in the absence of any of the molecules in the containers.
  • an entire thermal denaturation curve can be compared to other entire thermal denaturation curves using computer analytical tools.
  • combinatorial library refers to a plurality of molecules or compounds which are formed by combining, in every possible way fore given compound length, a set of chemical or biochemical building blocks which may or may not be related in structure. Alternatively, the term can refer to a plurality of chemical or biochemical compounds which are formed by selectively combining a particular set of chemical building blocks.
  • Combinatorial libraries can be constructed according to methods familiar to those skilled in the art. For example, see Rapoport et al., Immunology Today 16:43-49 (1995); Sepetov, N. F. et al., Proc. Natl. Acad. Sci. U.S.A. 92:5426-5430 (1995); Gallop, M. A.
  • combinatorial library refers to a DirectedDiversity library, as set forth in U.S. Pat. No. 5,463,564. Regardless of the mariner in which a combinatorial library is constructed, each molecule or compound in the library is catalogued for future reference.
  • compound library refers to a plurality of molecules or compounds which were not formed using the combinatorial approach of combining chemical or biochemical building blocks. Instead, a compound library is a plurality of molecules or compounds which are accumulated and are stored for use in future ligand-receptor binding assays. Each molecule or compound in the compound library is catalogued for future reference.
  • multiplicity of molecules refers to at least two molecules, compounds, or containers.
  • multi-variable refers to more than one experimental variable.
  • screening refers to the testing of a multiplicity of molecules or compounds for their ability to bind to a target molecule which is capable of denaturing.
  • the term “ranking” refers to the ordering of the affinities of a multiplicity of molecules or compounds for a target molecule, according to the ability of the molecule or compound to shift the thermal denaturation curve of the target molecule, relative to the thermal denaturation curve of the target molecule in the absence of any molecule or compound.
  • the term “ranking” also refers to the ordering of the efficacies of a multiplicity of biochemical conditions in optimizing protein stabilization, protein folding, protein crystallization, or protein shelf life.
  • the term “ranking” refers to the ordering of the efficacies of one or more combinations of biochemical conditions to shift the thermal denaturation curve of the target molecule, relative to the thermal denaturation curve of the target molecule under a reference set of conditions.
  • reference set of conditions refers to a set of biochemical conditions under which a thermal denaturation curve for a target molecule is obtained. Thermal denaturation curves obtained under conditions different than the reference conditions are compared to each other and to the thermal denaturation curve obtained for the target molecule under reference conditions.
  • molecules, compounds, or biochemical conditions are preferable.
  • molecules, compounds, or biochemical conditions can be ranked for their ability to stabilize a target molecule according to the change in entire thermal denaturation curve.
  • lead molecule refers to a molecule or compound, from a combinatorial library, which displays relatively high affinity for a target molecule.
  • the terms “lead compound” and “lead molecule” are synonymous.
  • the term “relatively high affinity” relates to affinities in the K d range of from 10 ⁇ 4 to 10 ⁇ 15 M.
  • target molecule encompasses peptides, proteins, nucleic acids, and other receptors.
  • the term encompasses both enzymes and proteins which are not enzymes.
  • the term encompasses monomeric and multimeric proteins. Multimeric proteins may be homomeric or heteromeric.
  • the term encompasses nucleic acids comprising at least two nucleotides, such as oligonucleotides. Nucleic acids can be single-stranded, double-stranded or triple-stranded.
  • the term encompasses a nucleic acid which is a synthetic oligonucleotide, a portion of a recombinant DNA molecule, or a portion of chromosomal DNA.
  • target molecule also encompasses portions of peptides, proteins, and other receptors which are capable of acquiring secondary, tertiary, or quaternary structure through folding, coiling or twisting.
  • the target molecule may be substituted with substituents including, but not limited to, cofactors, coenzymes, prosthetic groups, lipids, oligosaccharides, or phosphate groups.
  • the term “capable of denaturing” refers to the loss of secondary, tertiary, or quaternary structure through unfolding, uncoiling, or untwisting.
  • target molecule and “receptor” are synonymous.
  • target molecules are included, but not limited to those disclosed in Faisst, S. et al., Nucleic Acids Research 20:3-26 (1992); Pimentel, E., Handbook of Growth Factors, Volumes I-III, CRC Press, (1994); Gilman, A. G. et al., The Pharmacological Basis of Therapeutics, Pergamon Press (1990); Lewin, B., Genes V, Oxford University Press (1994); Roitt, I., Essential Immunology, Blackwell Scientific Publ. (1994); Shimizu, Y., Lymphocyte Adhesion Molecules, R G Austin (1993); Hyams, J. S.
  • target molecule refers more specifically to proteins involved in the blood coagulation cascade, fibroblast growth factors, and fibroblast growth factor receptors, urokinase, and factor D.
  • molecule refers to the compound which is tested for binding affinity for the target molecule. This term encompasses chemical compounds of any structure, including, but not limited to nucleic acids and peptides. More specifically, the term “molecule” encompasses compounds in a compound or a combinatorial library. The terms “molecule” and “ligand” are synonymous.
  • thermo change and “physical change” encompass the release of energy in the form of light or heat, the absorption of energy in the form or light or heat, changes in turbidity and changes in the polar properties of light.
  • the terms refer to fluorescent emission, fluorescent energy transfer, absorption of ultraviolet or visible light, changes in the polarization properties of light, changes in the polarization properties of fluorescent emission, changes in turbidity, and changes in enzyme activity.
  • Fluorescence emission can be intrinsic to a protein or can be due to a fluorescence reporter molecule (below).
  • fluorescence can be due to ethidium bromide, which is an intercalating agent.
  • the nucleic acid can be labeled with a fluorophore (below).
  • contacting a target molecule refers broadly to placing the target molecule in solution with the molecule to be screened for binding. Less broadly, contacting refers to the turning, swirling, shaking or vibrating of a solution of the target molecule and the molecule to be screened for binding. More specifically, contacting refers to the mixing of the target molecule with the molecule to be tested for binding. Mixing can be accomplished, for example, by repeated uptake and discharge through a pipette tip. Preferably, contacting refers to the equilibration of binding between the target molecule and the molecule to be tested for binding. Contacting can occur in the container (infra) or before the target molecule and the molecule to be screened are placed in the container.
  • the target molecule may be contacted with a nucleic acid prior to being contacted with the molecule to be screened for binding.
  • the target molecule may be complexed with a peptide prior to being contacted with the molecule to be screened for binding.
  • the target molecule may be phosphorylated or dephosphorylated prior to being contacted with the molecule to be screened for binding.
  • a carbohydrate moiety may be added to the target molecule before the target molecule is contacted with the molecule to be screened for binding.
  • a carbohydrate moiety may be removed from the target molecule before the target molecule is contacted with the molecule to be screened for binding.
  • the term “container” refers to any vessel or chamber in which the receptor and molecule to be tested for binding can be placed.
  • the term “container” encompasses reaction tubes (e.g., test tubes, microtubes, vials, etc.).
  • the term “container” refers to a well in a multiwell microplate or microtiter plate.
  • sample refers to the contents of a container.
  • a “thermal denaturation curve” is a plot of the physical change associated with the denaturation of a protein or a nucleic acid as a function of temperature. See, for example, Davidson et al., Nature Structure Biology 2:859 (1995); Clegg, R. M. et al., Proc. Natl. Acad. Sci. U.S.A . 90:2994-2998 (1993).
  • T m is the temperature midpoint of a thermal denaturation curve.
  • the T m can be readily determined using methods well known to those skilled in the art. See, for example, Weber, P. C. et al., J. Am. Chem. Soc. 116:2717-2724 (1994); Clegg, R. M. et al., Proc. Natl. Acad. Sci. U.S.A. 90:2994-2998 (1993).
  • fluorescence probe molecule refers to a fluorophore, which is a fluorescent molecule or a compound which is capable of binding to an unfolded or denatured receptor and, after excitement by light of a defined wavelength, emits fluorescent energy.
  • fluorescence probe molecule encompasses all fluorophores.
  • the term encompasses fluorophores such as thioinosine, and N-ethenoadenosine, formycin, dansyl derivatives, fluorescein derivatives, 6-propionyl-2-dimethylamino)-napthalene (PRODAN), 2-anilinonapthalene, and N-arylamino-naphthalene sulfonate derivatives such as 1-anilinonaphthalene-8-sulfonate (1,8-ANS), 2-anilinonaphthalene-6-sulfonate (2,6-ANS), 2-aminonaphthalene-6-sulfonate, N,N-dimethyl-2-aminonaphthalene-6-sulfonate, N-phenyl-2-aminonaphthalene, N-cyclohexyl-2-aminonaphthalene-6-sulfonate, N-phenyl-2-aminonaphthalene-6-sulfonate
  • a double-stranded oligonucleotide may be used in fluorescence resonance energy transfer assays.
  • One strand of the oligonucleotide will contain the donor fluorophore.
  • the other strand of the oligonucleotide will contain the acceptor fluorophore.
  • the fluorophore can be incorporated directly into the oligonucleotide sequence.
  • the fluorophore can be attached to either the 5′- or 3′-terminus of the oligonucleotide.
  • a donor fluorophore is one which, when excited by light, will emit fluorescent energy. The energy emitted by the donor fluorophore is absorbed by the acceptor fluorophore.
  • the term “donor fluorophore” encompasses all fluorophores including, but not limited to, carboxyfluorescein, iodoacetamidofluorescein, and fluorescein isothiocyanate.
  • the term “acceptor fluorophore” encompasses all fluorophores including, but not limited to, iodoacetamidoeosin and tetramethylrhodamine.
  • carrier encompasses a platform or other object, of any shape, which itself is capable of supporting at least two containers.
  • the carrier can be made of any material, including, but not limited to glass, plastic, or metal.
  • the carrier is a multiwell microplate.
  • microplate and microtiter plate are synonymous.
  • the carrier can be removed from the heating element. In the present invention, a plurality of carriers are used. Each carrier holds a plurality of containers.
  • biochemical conditions encompasses any component of a physical, chemical, or biochemical reaction. Specifically, the term refers to conditions of temperature, pressure, protein concentration, pH, ionic strength, salt concentration, time, electric current, potential difference, concentrations of cofactor, coenzyme, oxidizing agents, reducing agents, detergents, metal ion, ligands, or glycerol.
  • the term “denatured protein” refers to a protein which has been treated to remove secondary, tertiary, or quaternary structure.
  • the term “native protein” refers to a protein which possesses the degree of secondary, tertiary or quaternary structure that provides the protein with full chemical and biological function.
  • a native protein is one which has not been heated and has not been treated with denaturation agents or chemicals such as urea.
  • the term “denatured nucleic acid” refers to a nucleic acid which has been treated to remove folded, coiled, or twisted structure. Denaturation of a triple-stranded nucleic acid complex is complete when the third strand has been removed from the two complementary strands. Denaturation of a double-stranded DNA is complete when the base pairing between the two complementary strands has been interrupted and has resulted in single-stranded DNA molecules that have assumed a random form. Denaturation of single-stranded RNA is complete when intramolecular hydrogen bonds have been interrupted and the RNA has assumed a random, non-hydrogen bonded form.
  • folding refers to the acquisition of the correct secondary, tertiary, or quaternary structure, of a protein or a nucleic acid, which affords the full chemical and biological function of the biomolecule.
  • efficacy refers to the effectiveness of a particular set of biochemical conditions in facilitating the refolding or renaturation of an unfolded or denatured protein.
  • spectral measurement and “spectrophotometric measurement” refer to measurements of changes in the absorption of light. Turbidity measurements, measurements of visible light absorption, and measurement of ultraviolet light absorption are examples of spectral measurements.
  • polarimetric measurement relates to measurements of changes in the polarization properties of light and fluorescent emission.
  • Circular dichroism and optical rotation are examples of polarization properties of light which can be measured polarimetrically. Measurements of circular dichroism and optical rotation are taken using a spectropolarimeter. “Nonpolarimetric” measurements are those that are not obtained using a spectropolarimeter.
  • selection refers to a pool or a group of at least one molecule to be tested for binding to a target molecule or receptor.
  • a “host” is a bacterial cell that has been transformed with recombinant DNA for the purpose of expressing protein which is heterologous to the host bacterial cell.
  • the thermal shift assay is based on the ligand-dependent change in the thermal denaturation curve of a receptor, such as a protein or a nucleic acid. When heated over a range of temperatures, a receptor will unfold. By plotting the degree of denaturation as a function of temperature, one obtains a thermal denaturation curve for the receptor.
  • a useful point of reference in the thermal denaturation curve is the temperature midpoint (T m ), the temperature at which the receptor is half denatured.
  • Ligand binding stabilizes the receptor (Schellman, J., Biopolymers 14:999-1018 (1975)). The extent of binding and the free energy of interaction follow parallel courses as a function of ligand concentration (Schellman, J., Biophysical Chemistry 45:273-279 (1993); Barcelo, F. et al., Chem. Biol. Interactions 74:315-324 (1990)). As a result of stabilization by ligand, more energy (heat) is required to unfold the receptor. Thus, ligand binding shifts the thermal denaturation curve. This property can be exploited to determine whether a ligand binds to a receptor: a change, or “shift”, in the thermal denaturation curve, and thus in the T m , suggests that a ligand binds to the receptor.
  • thermodynamic basis for the thermal shift assay has been described by Schellman, J. A. ( Biopolymers 15:999-1000 (1976)), and also by Brandts et al. (Biochemistry 29:6927-6940 (1990)).
  • K L T m the ligand association constant at T m ;
  • T m the midpoint for the protein unfolding transition in the presence of ligand
  • T 0 the midpoint for the unfolding transition in the absence of ligand
  • ⁇ H u T 0 the enthalpy of protein unfolding in the absence of ligand at T 0 ;
  • ⁇ C pu the change in heat capacity upon protein unfolding in the absence of ligand
  • the parameters ⁇ H u and ⁇ C pu are usually observed from differential scanning calorimetry experiments and are specific for each receptor. To calculate the binding constant from equation 1, one should have access to a differential scanning calorimetry instrument to measure ⁇ H u and ⁇ C pu for the receptor of interest. One can also locate these parameters for the receptor of interest, or a receptor closely related to it, in the literature. In these situations, equation (1) will allow the accurate measurement of K L at T m .
  • K L T K L T m ⁇ exp ⁇ ⁇ - ⁇ ⁇ H L T R ⁇ [ 1 T - 1 T m ] + ⁇ ⁇ ⁇ C pL R ⁇ [ ln ⁇ ( T T m ) - T T m + 1 ] ⁇ ( equation ⁇ ⁇ 2 )
  • K L T the ligand association constant at any temperature T
  • K L T m the ligand association constant at T m ;
  • T m the midpoint for the protein unfolding transition in the presence of ligand
  • ⁇ H L T the enthalpy of ligand binding in the absence of ligand at T;
  • ⁇ C pL the change in heat capacity upon binding of ligand
  • K L T K L T m ⁇ exp ⁇ ⁇ - ⁇ ⁇ ⁇ H L T R ⁇ [ 1 T - 1 T m ] ⁇ ( equation ⁇ ⁇ 3 )
  • the present invention is particularly useful for screening a combinatorial or a compound library. To achieve high throughput screening, it is best to house samples on a multicontainer carrier or platform.
  • a multicontainer carrier facilitates the heating of a plurality of samples simultaneously.
  • a multiwell microplate for example a 96 or a 384 well microplate, which can accommodate 96 or 384 different samples, is used as the earner.
  • one sample is contained in each well of a multi-well microplate.
  • the control well contains receptor, but no molecule to be tested for binding.
  • Each of the other samples contains at least one molecule to be tested for binding.
  • the thermal denaturation curve for the receptor in the control well is the curve against which curves for all of the other experiments are compared.
  • the rate of screening is accelerated when the sample contains more than one molecule to be tested for binding. For example, the screening rate is increased 20-fold when the sample contains a pool of 20 molecules. Samples which contain a binding molecule must then be divided into samples containing a smaller collection of molecules to be tested for binding. These divided collections must then be assayed for binding to the target molecule. These steps must be repeated until a single molecule responsible for the original thermal shift is obtained.
  • Receptor denaturation can be measured by light spectrophotometry.
  • a protein in solution denatures in response to heating, the receptor molecules aggregate and the solution becomes turbid.
  • Thermally induced aggregation upon denaturation is the rule rather than the exception. Aggregation generally complicates calorimetric experiments. Aggregation, however, is an advantage when, using a spectrophotometric technology, because changes in turbidity can be measured by monitoring the change in absorbance of visible or ultraviolet light of a defined wavelength.
  • Denaturation of a nucleic acid can be monitored using light spectrophotometry.
  • the change in hyperchromicity which is the increase in absorption of light by polynucleotide solutions due to a loss of ordered structure, is monitored as a function of increase in temperature. Changes in hyperchromicity is typically assayed using light spectrophotometry.
  • fluorescence spectrometry is used to monitor thermal denaturation.
  • the fluorescence methodology is more sensitive than the absorption methodology.
  • fluorescence spectrometry can be performed using an ethidium bromide displacement assay (Lee, M. et al., J. Med. Chem. 36:863-870 (1993)).
  • ligand binding displaces ethidium bromide and results in a decrease in the fluorescent emission from ethidium bromide.
  • An alternative approach is to use fluorescence resonance emission transfer. In the latter approach, the transfer of fluorescent energy, from a donor fluorophore on one strand of an oligonucleotide to an acceptor fluorophore on the other strand, is monitored by measuring the emission of the acceptor fluorophore. Denaturation prevents the transfer of fluorescent energy.
  • the element upon which the sample carrier is heated can be any element capable of heating samples rapidly and in a reproducible fashion.
  • a plurality of samples is heated simultaneously.
  • the plurality of samples can be heated on a single heating element.
  • the plurality of samples can be heated to a given temperature on one heating element, and then moved to another heating element for heating to another temperature. Heating can be accomplished in regular or irregular intervals.
  • the samples should be heated evenly, in intervals of 1 or 2° C.
  • the temperature range across which the samples can be heated is from 25 to 110° C. Spectral readings are taken after each heating step.
  • Samples can be heated and read by the spectral device in a continuous fashion: Alternatively, after each heating step, the samples may be cooled to a lower temperature prior to taking the spectral readings. Preferably, the samples are heated continuously and spectral readings are taken while the samples are being heated.
  • Spectral readings can be taken on all of the samples in the carrier simultaneously. Alternatively, readings can be taken on samples in groups of at least two at a time. Finally, the readings can be taken one sample at a time.
  • thermal denaturation is monitored by fluorescence spectrometry using an assay apparatus such as the one shown in FIG. 29.
  • the instrument consists of a scanner and a control software system.
  • the system is capable of quantifying soluble and cell-associated fluorescence emission. Fluorescence emission is detected by a photomultiplier tube in a light-proof detection chamber.
  • the software runs on a personal computer and the action of the scanner is controlled through the software.
  • a precision X-Y mechanism scans the microplate with a sensitive fiber-optic probe to quantify the fluorescence in each well.
  • the microplate and samples can remain stationary during the scanning of each row of the samples, and the fiber-optic probe is then is moved to the next row.
  • the microplate and samples can be moved to position a new row of samples under the fiber-optic probe.
  • the scanning system is capable of scanning 96 samples in under one minute.
  • the scanner is capable of holding a plurality of excitation filters and a plurality of emission filters to measure the most common fluorophores.
  • fluorescence emission readings can be taken one sample at a time, or on a subset of samples simultaneously.
  • An alternate embodiment of the assay apparatus is shown in FIG. 33. The assay apparatus of the present invention will be described in more detail below.
  • the present invention is also directed to a product of manufacture which comprises a carrier having a multiplicity of containers within it.
  • the product of manufacture can be used to screen a combinatorial library for lead compounds which bind to the receptor of interest
  • the combinatorial library can be screened using the method according to the present invention.
  • each of the containers contains a uniform amount of a receptor of interest
  • each of these containers contains a different compound from a combinatorial library at a concentration which is at least 2-fold above the concentration of the receptor.
  • the product of manufacture is a multiwell microplate or a multiplicity of multiwell microplates.
  • the receptor is a protein
  • each container may further contain a fluorescence probe molecule.
  • the receptor is a nucleic acid
  • each container may further contain ethidium bromide.
  • the nucleic acid may be labeled with a fluorophore.
  • the product of manufacture can be stored in any manner necessary to maintain the integrity of the receptor of interest.
  • the product of manufacture can be stored at a temperature between ⁇ 90° C. and room temperature.
  • the receptor and compound can be stored in lyophilized form, in liquid form, in powdered form, or can be stored in glycerol.
  • the product of manufacture may be stored either in the light or in the dark.
  • the heat conducting element or block upon which the sample carrier is heated can be any element capable of heating samples rapidly and reproducibly.
  • the plurality of samples can be heated on a single heating element.
  • the plurality of samples can be heated to a given temperature on one heating element, and then moved to another heating element for heating to another temperature. Heating can be accomplished in regular or irregular intervals.
  • the samples should be heated evenly, in intervals of 1 or 2° C.
  • the temperature range across which the samples can be heated is from 25 to 110° C.
  • a plurality of samples is heated simultaneously. If samples are heated in discrete temperature intervals, in a stairstep fashion, spectral readings are taken after each heating step. Alternatively, after each heating step, the samples may be cooled to a lower temperature prior to taking the spectral readings. Alternatively, samples can be heated in a continuous fashion and spectral readings are taken during heating.
  • Spectral readings can be taken on all of the samples on a carrier simultaneously. Alternatively, readings can be taken on samples in groups of at least two at a time.
  • the present invention also provides an improved method for generating lead compounds. After a compound or a combinatorial library of compounds has been screened using the thermal shift assay, compounds which bind to the target receptor are chemically modified to generate a second library of compounds. This second library is then screened using the thermal shift assay. This process of screening and generating a new library continues until compounds that bind to the target receptor with affinities in the K d range of from 10 ⁇ 4 to 10 ⁇ 15 M are obtained.
  • a fluorescence emission imaging system can be used to monitor the thermal denaturation of a target molecule or a receptor. Fluorescence emission imaging systems are well known to those skilled in the art.
  • the AlphaImagerTM Gel Documentation and Analysis System (Alpha Innotech, San Leandro, Calif.) employs a high performancd charge coupled device camera with 768 ⁇ 494 pixel resolution. The charge coupled device camera is interfaced with a computer and images are anlayzed with Image analysis softwareTM.
  • the ChemiImagerTM (Alpha Innotech) is a cooled charge coupled device that performs all of the functions of the AlphaImagerTM and in addition captures images of chemiluminescent samples and other low intensity samples.
  • the ChemiImagerTM charge coupled device includes a Pentium processor (1.2 Gb hard drive, 16 Mb RAM), AlphaEaseTM analysis software, a light tight cabinet, and a UV and white light trans-illuminator.
  • a Pentium processor 1.2 Gb hard drive, 16 Mb RAM
  • AlphaEaseTM analysis software a light tight cabinet
  • a UV and white light trans-illuminator a UV and white light trans-illuminator.
  • the MRC-1024 UV/Visible Laser Confocal Imaging System facilitates the simultaneous imaging of more than one fluorophore across a wide range of illumination wavelengths (350 to 700 nm).
  • the Gel Doc 1000 Fluorescent Gel Documentation System (BioRad, Richmond, Calif.) can clearly display sample areas as large as 20 ⁇ 20 cm, or as small as 5 ⁇ 4 cm. At least two 96 well microplates can fit into a 20 ⁇ 20 cm area.
  • the Gel Doc 1000 system also facilitates the performance of time-based experiments.
  • a fluorescence thermal imaging system can be used to monitor receptor unfolding in a microplate thermal shift assay.
  • a plurality of samples is heated simultaneously between 25 to 110° C.
  • a fluorescence emission reading is taken for each of the plurality of samples simultaneously.
  • the fluorescence emission in each well of a 96 or a 384 well microplate can be monitored simultaneously.
  • fluorescence emission readings can be taken continuously and simultaneously for each sample.
  • all samples display a low level of fluorescence emission. As the temperature is increased, the fluorescence in each sample increases.
  • a thermal shift assay can be performed in a volume of 100 ⁇ L volumes. For the following reasons, however, it is preferable to perform a thermal shift assay in a volume of 10 ⁇ L.
  • a thermal shift assay in a volume of 10 ⁇ L.
  • approximately 10-fold less protein is required for the miniaturized assay.
  • only ⁇ 5 to 40 pmole of protein are required (0.1 ⁇ g to 1.0 ⁇ g for a 25 kDa protein) for the assay (i.e. 5 to 10 ⁇ L working volume with a target molecule concentration of about 1 to about 4 ⁇ M).
  • 1 mg of protein can be used to conduct 1,000 to 10,000 assays in the miniaturized format This is particularly advantageous when the target molecule is available in minute quantities.
  • the ideal ligand concentration is about 50 ⁇ M, which translates into 250 pmoles of ligand, or 100 ng (assuming a MW of 500 Da) of ligand per assay in the miniaturized format.
  • the smaller working volume allows the potential of using larger arrays of assays because the miniaturized assay can fit into a much smaller area.
  • a 384 well (16 ⁇ 24 array) or 864 well (24 ⁇ 36 array) plates have roughly the same dimensions as the 96 well plates (about 8.5 ⁇ 12.5 cm).
  • the 384 well plate and the 864 well plate allows the user to perform 4 and 9 times as many assays, respectively, as can be performed using a 96 well plate.
  • 1536 well plates 32 ⁇ 48 arrays; Matrix Technologies Corp.
  • a 1536 well plate will facilitate sixteen times the throughput afforded by a 96 well plate.
  • the assay speed can be increased by about 16 times, relative to the speed at which the assay can be performed using the 96 well format.
  • the 8 ⁇ 12 assay array arrangement (in a 96-well plate) facilitates the performance of 96 assays/hr, or about 2300 assays/24 hours.
  • the 32 ⁇ 48 array assay arrangement facilitates the performance of about 1536 assays hr., or about 37,000 assays/24 hours can be performed using a 32 ⁇ 48 assay array configuration.
  • the assay volume can be 1-100 ⁇ L.
  • the assay volume is 1-50 ⁇ L. More preferably, the assay volume is 1-25 ⁇ L. More preferably still, the assay volume is 1-10 ⁇ L. More preferably still, the assay volume is 1-5 ⁇ L. More preferably still, the assay volume is 5 ⁇ L. Most preferably, the assay volume is 1 ⁇ L or 2 ⁇ L.
  • the assay is performed in V-bottom polycarbonate plates or polycarbonate dimple plates.
  • a dimple plate is a plate that contains a plurality of round-bottom wells that hold a total volume of 15 ⁇ L.
  • One alternative to taking spectral readings over a temperature range around the T m of the therapeutic target to obtain a full thermal unfolding curve for the ligand/target complex, in order to identify shifts in T m is to perform the assay at a single temperature near the T m of the target molecule.
  • samples that emit less fluorescence, relative to a control sample (containing a target molecule, but no candidate ligand) indicate that the candidate ligand binds to the target molecule.
  • the magnitude of a physical change associated with the thermal denaturation of a target molecule resulting from heating is determined by generating a thermal denaturation curve for the target molecule as a function of temperature over a range of one or more discrete or fixed temperatures.
  • the physical change associated with thermal denaturation for example, fluorescence emission, is measured.
  • the magnitude of the physical change at the discrete or fixed temperature for the target molecule in the absence of any ligand is noted.
  • the magnitude of the physical change in the presence of each of a multiplicity of different molecules, for example, combinatorial compounds, is measured.
  • the magnitude of the physical change associated with thermal denaturation of the target molecule in the presence of each of the multiplicity of molecules is compared to magnitude of the physical change obtained for the target molecule at the discrete or fixed temperature in the absence of any of the multiplicity of different molecules.
  • the affinities of the multiplicity of different molecules are ranked according to the change in the magnitude of the physical change.
  • the discrete or fixed temperature at which the physical change is measure can be any temperature that is useful for discriminating shifts in thermal stability.
  • the discrete or fixed temperature is the midpoint temperature T m for the thermal denaturation curve for the target molecule in the absence of any of the multiplicity of different molecules tested for binding to the target molecule.
  • the single temperature configuration is particularly advantageous if one is interested in assaying a series of relatively high affinity ligands, which are the preferred compounds for candidates in clinical testing. In cases where a less stringent requirement for binding affinity is preferred, however, one may increase the ligand concentration to 500 ⁇ M in order to identify ligands with K d 's of 2.5 ⁇ M or higher affinity.
  • the single temperature embodiment offers a number of advantages.
  • assay speed is increased by a factor often fold.
  • the single temperature variation will facilitate about 1000 assays per hr.
  • Using a 1536 well plate (32 ⁇ 48 array) as long as sample aliquoting can be effected at the same rate for the 32 ⁇ 48 array system as in the 8 ⁇ 12 array system, about 15,000 assays can be performed per hour.
  • Another alternative method for detecting the thermal unfolding transitions for the microplate thermal shift assay is through the intrinsic tryptophan (Trp) fluorescence of the target protein.
  • Terp tryptophan
  • the Biolumin 960 (Molecular Dynamics) uses a Xenon-Arc lamp. The Xenon-Arc lamp affords excitation at 280 nm and the measurement of emission at 350 nm.
  • the methods and assay apparatus of the present invention are not limited to assaying ligand-protein interactions.
  • the methods and the assay apparatus can be used to rapidly assay any multi-variable system related to protein stabilization.
  • the methods and the assay apparatus of the present invention can be used to simultaneously assay the binding of more than one compound or ligand to a target molecule. Using this approach, the additive effect of multiple-ligand binding can be assessed. Positive and negative cooperativity can be determined.
  • thermal shift assays are performed for a target molecule, such as a protein, in the absence of any ligands, in the presence of a single ligand, and in the presence of two or more ligands.
  • a thermal denaturation curve is generated for the protein alone and for each combination of protein and ligand(s).
  • the midpoint temperature T m is then determined for each curve.
  • Each T m is then compared to each of the other T m 's for the other curves.
  • each entire thermal denaturation curve is compared to each of the other thermal denaturation curves. In either of these manners, the additive contribution of more than one ligand to binding interaction or to protein stability can be determined.
  • the additive contributions of one or more biochemical conditions to protein stability can be determined.
  • the present invention can be used to rapidly identify biochemical conditions that optimize protein stabililty, and hence shelf-life. of a protein.
  • the methods and the assay apparatus of the present invention can be used to rank the efficacies of various biochemical conditions for refolding or renaturing an unfolded or denatured protein.
  • This embodiment addresses the need in the art for a reliable method for screening for effective refolding or renaturing conditions.
  • expression of recombinant DNA in a bacterial cell usually results in the sequestration of recombinant protein into bacterial inclusion bodies (Marston, F. A. O., Biochem. J. 240:1-12 (1986)).
  • expression in bacterial cells remains the method of choice for the high-level production of recombinant proteins (Rudolph, R., Protein Engineering: Principles and Practices, pp. 283-298, John Wiley & Sons (1995)).
  • recovery of recombinant protein requires that protein be isolated from inclusion bodies. Protein purification from inclusion bodies process necessitates the denaturation of recombinant protein.
  • recombinant protein must be renatured or refolded under conditions suitable to generate the protein in its native, fully functional form.
  • denatured protein In each of these cases, denatured protein must be renatured or refolded in order to be useful for further study or use. Unfortunately, one cannot easily predict the exact conditions under which a given protein or fragment of the protein should be renatured. Each protein is different. One must always resort to testing a number of different combinations of renaturing conditions before one can know which set of conditions is optimal. Thus, it is desirable to have a reliable and rapid method for ranking the efficacies of various renaturing conditions.
  • the function of the chaperonin is to partly unfold misfolded proteins (that is, kinetically trapped intermediates) with some of the energy of ATP hydrolysis being channeled into the conformational energy of the substrate polypeptide, forcing the polypeptide into a higher energy state from which it could once again attempt to refold correctly after being released into solution (Todd, M. J. et al., Science 265:659-666 (1994); Jackson, et al., Biochemistry 32:2554-2563 (1993); Weissman, J. S., et al., Cell 78:693-702 (1994); Weissman, J. S., & Kim, P. S., Science 253:1386-1393 (1991)).
  • pH can be understood to influence the folding reaction by its effect on the long range electrostatic interactions summed in the fourth term of the equation (4).
  • ⁇ g i,int short range interactions (H-bonds, van der Walls interactions, salt bridges, cofactor binding, etc.);
  • Glycerol alters the solvation properties of water to favor the native conformation of proteins.
  • the mechanism by which this occurs is the co-solvent exclusion and preferential hydration of the protein, not unlike the effect of salts of the salts of the Hofmeister series (Timasheff & Arakawa, In: Protein Structure, A Practical Approach , T. E. Creighton, ed., IRL Press, Oxford, UK (1989), pp. 331-354).
  • biochemical parameters that have been shown to affect protein folding are: protein concentration, temperature, glutathione redox buffers (GSH, GSSG), the presence of detergents, and the presence of other additives, such as glycerol, arginine-HCl, polyethylene glycol (PEG), and organic solvents.
  • a polyionic arginine tag metholdology for immobilizing and refolding a-glucosidase is disclosed in Stempfer, G. et al., Nature Biotechnology 14:329-334 (1996).
  • the thermal shift assay is used to rank the efficacy of various refolding or renaturing conditions.
  • a multiplicity of aliquots of a protein of interest which has been incubated under a variety of different biochemical folding conditions, are placed in a container in a multicontainer carrier.
  • An aliquot of the native, fully functional protein of known concentration is placed in the control container.
  • the samples can be placed in any multicontainer carrier.
  • each sample can be placed in a well of a multiwell microplate.
  • the present invention can be used to rank the efficacies of refolding or renaturing conditions.
  • Such conditions include, but are not limited to, the concentration of glycerol, the concentration of protein, the use of agents which catalyze the formation of disulfide bond formation, temperature, pH, ionic strength, type of solvent, the use of thiols such as reduced glutathione (GSH) and oxidized glutathione (GSSG), chaotropes such as urea, guanidinium chlorides, alkyl-urea, organic solvents such as carbonic acid amides, L-arginine HCl, Tris buffer, polyethylene glycol, nonionic detergents, ionic detergents, zwitterionic detergents, mixed micelles, and a detergent in combination with cyclodextrin.
  • the present invention can be used regardless of whether a denaturation agent is removed from the protein using dialysis, column chromatographic techniques, or suction filtration.
  • the conditions which facilitate optimal protein refolding can be determined rapidly.
  • the renatured protein samples and a control protein sample i.e., a sample of native protein in its fully functional form
  • a control protein sample i.e., a sample of native protein in its fully functional form
  • a spectral reading is taken.
  • spectral readings can be taken during a continuous, pre-determined temperature profile.
  • a thermal denaturation curve is constructed for each sample. The T m for the thermal denaturation curve of the native, fully functional protein is determined.
  • the relative efficacies of the refolding conditions are ranked according to the magnitude of the physical change associated with unfolding at the T m of the native, fully functional protein, relative to the magnitude of the physical change of a known quantity of the native, fully functional protein at that T m .
  • the magnitude of physical change used to measure the extent of unfolding corresponds to the amount of correctly folded protein.
  • the present invention provides a method for screening biochemical conditions that facilitate and optimize protein folding.
  • To screen conditions for a given protein it is first necessary to determine the thermal unfolding profile for a protein of interest. This is accomplished by generating a denaturation curve using the microplate thermal shift assay.
  • Various conditions can be optimized, including pH optimum, ionic strength dependence, concentration of salts of the Hofmeister series, sucrose concentration, arginine concentration, dithiothreitol concentration, metal ion concentration, etc.
  • biochemical conditions have an additive effect on protein stability. Once a set of biochemical conditions that facilitate an increase in protein stability have been identified using the thermal shift assay, the same set of conditions can be used in protein folding experiments with recombinant protein. See FIG. 27. If the conditions that promote protein stability in the thermal shift assay correlate with conditions that promote folding of recombinant protein, conditions can be further optimized by performing additional thermal shift assays until a combination of stabilizing conditions that result in further increase protein stability are identified. Recombinant protein is then folded under those conditions. This process is repeated until optimal folding conditions are identified. Protein stability is expected to correlate with improved yields of protein folding. Yield of correctly folded protein can be determined using any suitable technique.
  • yield of correctly folded protein can be calculated by passing refolded protein over an affinity column, for example, a column to which a ligand of the protein is attached, and quantifying the amount of protein that is present in the sample.
  • folding conditions can be assessed for their additive contributions to correct folding.
  • the transition state for the protein folding reaction resembles the native form of the protein more than the denatured form. This has been demonstrated to be the case for may proteins (Fersht, A. R., Curr. Op. Struct. Biol . 7:3-9 (1997)).
  • the methods and the apparatus of the present invention provide a rapid, high throughput approach to screening for combinations of biochemical conditions that favor the protein folding.
  • the method does not require cumbersome and time consuming steps that conventional approaches to protein folding require.
  • it is not necessary to dilute protein to large volumes and low protein concentrations ( ⁇ 10 ⁇ g/mL) in order to avoid aggregation problems associated with conventional methods of recombinant protein refolding. Suppression of protein aggregation will allow for screening biochemical parameters that shift the protein folding equilibrium (between the unfolded and the folded forms of proteins) to the correct native conformation.
  • the methods and the assay apparatus of the present invention are also useful for determining conditions that facilitate protein crystallization.
  • the crystallization of molecules from solution is a reversible equilibrium process, and the kinetic and thermodynamic parameters are a function of the chemical and physical properties of the solvent system and solute of interest (McPherson, A., In: Preparation and Analysis of Protein Crystals , Wiley Interscience (1982); Weber, P. C., Adv. Protein Chem . 41:1-36 (1991)) 1991).
  • the solute is partitioned between the soluble and solid phase instead of the unfolded and native states.
  • protein crystallization can be viewed as a higher level variation of protein folding where whole molecules are packed to maximize cohesive energies instead of individual amino acid residues.
  • the composition of the solvent can make very important contributions to the extent of partitioning between the soluble (unfolded) and crystalline (native) forms.
  • the cohesive interactions present in protein macromolecules and the role played by solvent in modulating these interactions for both protein folding and protein crystallization are complex and not fully understood at the present time.
  • biochemical conditions that promote protein stabililty and protein folding also promote protein crystallization.
  • biochemical conditions that were found to increase the stability of D(II) FGF receptor 1 correlate with the conditions that facilitated the crystallization of x-ray diffraction quality protein crystals.
  • Conditions that were employed to obtain crystals of D(II) FGFR1 protein are shown in Table 1. Protein crystals were obtained in the pH range 7.4 to 9.2 in the presence of the Hofmeister salt Li 2 SO 4 (65 to 72%). These crystallization conditions correlated with the pH optimum of about 8.0 in FIG. 23.
  • FIGS. 17 A-D and 18 show the results of microplate thermal shift assays of conditions that facilitate human ⁇ -thrombin stability.
  • Table 2 contains a summary of the conditions identified by three different investigators that facilitate crystallization of x-ray diffraction quality human ⁇ -thrombin crystals (Bode, W., et al., Protein Sci . 1:426-471 (1992); Vijayalakshmi, J. et al., Protein Sci . 3:2254-22271 (1994); and Zdanov, A. et al., Proteins: Struct. Funct. Genet . 17:252-265 (1993)).
  • Protein crystallization is a slow and tedious process that has historically been the rate determining step for the x-ray diffraction determination of protein and nucleic acid structures.
  • the method and apparatus of the present invention facilitate the rapid, high-throughput elucidation of conditions that promote the stability of a given protein and thus the formation of X-ray quality protein crystals.
  • the assay apparatus of the present invention is directed to an automated temperature adjusting and spectral emission receiving system that simultaneously adjusts the temperature of a multiplicity of samples over a defined temperature range and receives spectral emission from the samples.
  • the assay apparatus of the present invention is particularly useful for performing microplate thermal shift assays of protein stability.
  • the assay apparatus of the present invention can be used to practice all of the methods of the present invention.
  • the assay apparatus of the present invention replaces separate heating devices and spectral emission receiving devices.
  • the assay apparatus of the present invention can be configured to simultaneously adjust the temperature of a multiplicity of samples and receive spectral emissions from the samples during adjustment of temperature in accordance with a predetermined temperature profile.
  • the assay apparatus of the present invention includes a sensor which is positioned over a movable heat conducting block upon which an array of samples is placed.
  • a relative movement means such as a servo driven armature, is used to move the sensor so that the sensor is sequentially positioned over each sample in the array of samples.
  • the sensor receives spectral emissions from the samples.
  • the assay apparatus of the present invention can be configured so that it contains a single heat conducting block.
  • the assay apparatus can be configured so that it contains a plurality of heat conducting blocks upon a movable platform.
  • the platform may be a translatable platform that can be translated, for example, by a servo driven linear slide device.
  • An exemplary linear slide device is model SA A5M400 (IAI America, Torrance, Calif.).
  • the sensor receives spectral emissions from each of the samples on a given heat conducting block.
  • the platform is then translated to place another heat conducting block and its accompanying samples under the sensor so that it receives spectral emissions from each of the samples on that heating block.
  • the platform is translated until spectral emissions are received from the samples on all heat conducting blocks.
  • the platform may by a rotatable platform that may be rotated, for example, by a servo driven axle.
  • the sensor receives spectral emissions from each of the samples on a given heat conducting block.
  • the platform is then rotated to place another heat conducting block and its accompanying samples under the sensor so that it receives spectral emissions from each of the samples on that heating block.
  • the platform is rotated until spectral emissions are received from the samples on all heat conducting blocks.
  • FIG. 29 shows a schematic diagram of one embodiment of an assay apparatus 2900 of the present invention.
  • Assay apparatus 2900 includes a heat conducting block 2912 that includes a plurality of wells 2920 for a plurality of samples 2910 .
  • Heat conducting block 2912 is composed of a material that has a relatively high coefficient-of thermal conductivity, such as aluminum, stainless steel, brass, teflon, and ceramic.
  • heat conducting block 2912 can be heated and cooled to a uniform temperature but will not be thermally conductive enough to require excess heating or cooling to maintain a temperature.
  • Assay apparatus 2900 also includes a light source 2906 for emitting an excitatory wavelength of light, shown generally at 2916 , for the samples.
  • Light source 2906 excites samples 2910 with excitatory light 2916 .
  • Any suitable light source can be used.
  • a tungsten-halogen lamp can be used.
  • a Xenon-arc lamp such as the Biolumin 960 (Molecular Dynamics) can be used.
  • Hg Lamp a high pressure mercury (Hg) Lamp can be used.
  • High pressure mercury lamps emit light of higher intensity than Xenon (Xe) lamps.
  • the intensity of light from a high pressure mercury lamp is concentrated in specific lines, and are only useful if the Hg lines are at suitable wavelengths for excitation of particular fluorophores.
  • Some fluorescent plate readers employ lasers for excitation in the visible region of the electromagnetic spectrum.
  • the FluorImagerTM Molecular Dynamics, Palo Alto, Calif.
  • This technology is useful when using fluorescent dyes that absorb energy at around 480 nm and emit energy at around 590 nm. Such a dye could then be excited with the 488 nm illumination of standard argon, argon/krypton lasers.
  • 1,1-dicyano-2-[6-(di-methylamino)naphthalen-2-yl]propene (DDNP) is such a dye.
  • DDNP 1,1-dicyano-2-[6-(di-methylamino)naphthalen-2-yl]propene
  • the advantage in using a laser is that a laser is characterized by very high intensity light, which results in an improved signal to noise ratio.
  • Excitatory light 2916 causes a spectral emission 2918 from samples 2910 .
  • Spectral emission 2918 can be electromagnetic radiation of any wavelength in the electromagnetic spectrum.
  • spectral emission 2918 is fluorescent, ultraviolet, or visible light.
  • spectral emission 2918 is fluorescence emission.
  • Spectral emission 2918 is received by a photomultiplier tube 2904 .
  • Photomultiplier tube 2904 is communicatively and operatively coupled to a computer 2914 by an electrical connection 2902 .
  • Computer 2914 functions as a data analysis means for analyzing spectral emission as a function of temperature.
  • the spectral receiving means or sensor of the assay apparatus of the present invention can comprise a photomultiplier tube.
  • the spectral receiving means or sensor can include a charge coupled device or a charge coupled device camera.
  • the spectral receiving means or sensor can include a diode array.
  • FIG. 30 An alternate embodiment of the assay apparatus of the present invention is shown in FIG. 30.
  • a charge coupled device (CCD) camera 3000 is used to detect spectral emission 2918 from samples 2910 .
  • CCD camera 3000 can be any CCD camera suitable for imaging fluorescent emissions.
  • suitable CCD cameras are available from Alpha-Innotech (San Leandro, Calif.), Stratagene (La Jolla, Calif.), and BioRad (Richmond, Calif.).
  • a charge coupled device CCD
  • high resolution CCD cameras can detect very small amounts of electromagnetic energy, whether it originates from distance stars, is diffracted by crystals, or is emitted by fluorophores.
  • a CCD is made of semi-conducting silicon. When photons of light fall on it, free electrons are released.
  • a CCD camera is particularly suitable for fluorescence emission imaging because it can detect very faint objects, affords sensitive detection over a broad spectrum range, affords low levels of electromagnetic noise, and detects signals over a wide dynamic range—that is, a charge coupled device can simultaneously detect bright objects and faint objects.
  • the output is linear so that the amount of electrons collected is directly proportional to the number of photons received. This means that the image brightness is a measure of the real brightness of the object, a property not afforded by, for example, photographic emulsions.
  • excitatory light 2916 can be a suitable lamp that is positioned over the plurality of samples 2910 .
  • excitatory light 2916 can be a suitable lamp that is positioned under the plurality of samples 2910 .
  • excitatory light 2916 can be delivered to each sample 2910 by a plurality of fiber optic cables. Each fiber optic cable is disposed through one of a plurality of tunnels in conducting block 2912 . Thus, each of samples 2910 receives excitatory light 2916 through a fiber optic cable.
  • source 2906 excites samples 2910 with excitatory light 2916 .
  • Excitatory light 2916 causes spectral emission 2918 from samples 2910 .
  • Spectral emission 2918 is filtered through an emission filter 3002 .
  • Emission filter 3002 filters out wavelengths of spectral emission 2918 that are not to be monitored or received by CCD camera 3000 .
  • CCD camera 3000 receives the filtered spectral emission 2918 from all of samples 2910 simultaneously. For simplicity and ease of understanding, only spectral emissions form one row of samples 2910 are shown in FIG. 30.
  • CCD camera 3000 is communicatively and operatively coupled to computer 2914 by electrical connection 2902 .
  • FIG. 31 one embodiment of assay apparatus 2900 is shown in more detail. As shown in FIG. 31, many apparatus components are attached to a base 3100 .
  • a heat conducting block relative movement means 3128 is used to move heat conducting block 2912 in directions 3150 and 3152 .
  • Heat conducting block relative movement means 3128 is communicatively and operatively connected to a servo controller 3144 . Activation of heat conducting block relative movement means 3128 by servo controller 3144 moves heat conducting block 2912 in directions 3150 and 3152 .
  • Servo controller 3144 is controlled by a computer controller 3142 .
  • computer 2914 could be used to control servo controller 3144 .
  • a sensor is removably attached to a sensor armature 3120 .
  • An exemplary sensor is a fiber optic probe 3122 .
  • Fiber optic probe 3122 includes a fiber optic cable capable of transmitting receiving excitatory light 2916 to samples 2910 , and a fiber optic cable capable of receiving spectral emission 2918 from samples 2910 .
  • Electromagnetic radiation is transmitted from excitatory light source 2906 to fiber optic probe 3122 by excitatory light input fiber optic cable 3108 .
  • a spectral receiving means comprising photomultiplier tube 2904 is used to detect spectral emission from samples 2910 .
  • electromagnetic radiation is transmitted from fiber optic probe 3122 to photomultiplier tube 2904 by fiber optic cable 3110 .
  • CCD camera 3002 is used to detect spectral emission from samples 2910 .
  • fiber optic cable 3110 is not required.
  • a temperature sensor 3124 is removably attached to sensor armature 3120 . Temperature sensor 3124 is communicatively and operably linked to a temperature controller 3162 . Temperature sensor 3124 monitors the temperature of heat conducting block 2912 and feeds temperature information back to temperature controller 3162 . Temperature controller 3162 is connected to heat conducting block 2912 by a thermoelectric connection 3164 . Under the action of temperature controller 3162 , the temperature of heat conducting block 2912 can be increased, decreased, or held constant. Particularly, the temperature of heat conducting block 2912 can be changed by temperature controller 3162 in accordance with a pre-determined temperature profile. Preferably, temperature computer controller 3162 is implemented using a computer system such as that described below with respect to FIG. 37.
  • the term “temperature profile” refers to a change in temperature over time.
  • the term “temperature profile” encompasses continuous upward or downward changes in temperature, both linear and non-linear changes.
  • the term also encompasses any stepwise temperature change protocols, including protocols characterized by incremental increases or decreases in temperature during which temperature increases or decreases are interrupted by periods during which temperature is maintained constant.
  • the temperature profile can be pre-determined by programming temperature computer controller 3162 .
  • temperature profiles can be stored in a memory device of temperature controller 3162 , or input to temperature controller 3162 by an operator.
  • a sensor armature relative movement means 3130 is used to move sensor armature 3120 in directions 3154 and 3156 .
  • a sensor armature servo controller 3118 is fixedly connected to excitatory light filter housing 3160 . Activation of sensor armature servo controller 3118 moves fiber optic probe 3122 in directions 3154 and 3156 . It would be readily apparent to one of ordinary skill in the relevant art how to configure servo controllers to move heat conducting block 2912 and sensor armature 3120 . It should be understood that the present invention is not limited to the use of servo controllers for movement of heat conducting block 2912 and sensor armature 3120 , and other suitable means known to one of skill in the art can also be used, such as a motor.
  • Servo controllers 3118 and 3144 are both communicatively and operatively connected to computer controller 3142 .
  • Computer controller 3142 controls the movement of sensor armature 3120 in directions 3154 and 3156 .
  • computer controller 3142 controls the movement of heat conducting block relative movement means 3128 in directions 3150 and 3152 .
  • excitatory light source 2906 is used to excite samples 2910 .
  • Excitatory light source 2906 is communicatively and operably connected to excitatory light filter 3104 , which is contained within excitatory light filter housing 3160 .
  • Excitatory light filter 3104 filters out all wavelengths of light from excitatory light source 2906 except for the wavelength(s) of light that are desired to be delivered by fiber optic probe 3122 to samples 2910 .
  • An excitatory light filter servo controller 3106 controls the aperture of excitatory light filter 3104 .
  • Excitatory light source 2906 and excitatory light filter servo controller 3106 are communicatively and operatively connected to excitatory light computer controller 3102 .
  • Computer controller 3102 controls the wavelength of excitatory light transmitted to samples 2910 by controlling excitatory light filter servo controller 3106 .
  • Excitatory light 2916 is transmitted through excitatory light input fiber optic cable 3108 to fiber optic probe 3122 for transmission to samples 2912 .
  • Spectral emission : 2918 from samples 2910 is received by fiber optic probe 3122 and is transmitted to a spectral emission filter 3114 by output fiber optic cable 3110 .
  • Spectral emission filter 3114 is contained within a spectral emission filter housing 3166 .
  • Spectral emission filter housing 3166 is disposed on photomultiplier tube housing 3168 .
  • Photomultiplier tube housing 3168 contains photomultiplier tube 2904 .
  • a spectral emission servo controller 3112 controls the aperture of spectral emission filter 3114 , thereby controlling the wavelength of spectral emission 2918 that is transmitted to photomultiplier tube 2904 .
  • Spectral emission servo controller 3112 is controlled by a computer controller 3170 .
  • Spectral emission 2918 from samples 2910 is transmitted from photomultiplier tube 2904 .
  • Electrical output 3140 connects photomultiplier tube 2904 to electric connection 2902 .
  • Electric connection 2902 connects electrical output 3140 to computer 2914 .
  • computer 2914 processes the spectral emission signal from samples 2910 .
  • Exemplary software is a graphical interface that automatically analyzes fluorescence data obtained from samples 2910 .
  • Such software is well known to those of ordinary skill in the art.
  • the CytoFluorTMII fluorescence multi-well plate reader utilizes the CytocalcTM Data Analysis System (PerSeptive Biosystems, Framingham, Mass.).
  • Other suitable software includes, MicroSoft Excel or any comparable software.
  • FIGS. 32 A-C illustrate one embodiment of a thermal electric stage or heat conducting block for the assay apparatus of the present invention.
  • FIG. 32A shows a side view of heat conducting block 2912 and a heat conducting wire 3206 .
  • FIG. 32B shows a top view of heat conducting block 2912 and heat conducting wire 3206 .
  • Heat conducting wire 3206 is a temperature adjusting element that adjusts the temperature of heat conducting block 2912 .
  • temperature controller 3162 causes heat conducting wire 3206 to increase or decrease in temperature, thereby changing the temperature of heat conducting block 2912 .
  • an exemplary temperature controller is a resistance device that converts electric energy into heat energy.
  • the heating element can be a circulating water system, such as that disclosed in U.S. Pat. No. 5,255,976, the content of which is incorporated herein by reference.
  • the temperature adjusting element can be a heat conducting surface upon which heat conducting block 2912 is disposed.
  • the temperature of heat conducting wire 3206 can be changed by temperature controller 3162 in accordance with a pre-determined temperature profile.
  • Temperature controller 3162 is preferably implemented using a computer system such as that described below with respect to FIG. 37.
  • computer 2914 could be used to implement temperature controller 3162 .
  • An exemplary set of specifications for temperature controller 3162 and heat conducting block 2912 is as follows: resolution 0.1° C. accuracy +0.5° C. stability 0.1° C. repeatability 0.1° C.
  • Temperature controller 3162 changes temperature in accordance with a temperature profile as discussed below with respect to FIGS. 36A and 36B.
  • the temperature of heat conducting block 2912 can be controlled such that a uniform temperature is maintained across the heat conducting block.
  • the temperature of heat conducting block 2921 can be controlled such that a temperature gradient is established from one end of the heat conducting block to the other.
  • Heat conducting block 2912 is preferably configured with plurality of wells 2920 for samples 2910 to be assayed.
  • each of wells 2920 is configured to receive a container containing one of plurality of samples 2910 .
  • heat conducting block 2912 is configured to receive a container containing plurality of samples 2910 .
  • An exemplary container for containing plurality of samples 2910 is a microtiter plate.
  • heat conducting block 2912 is configured to receive a heat conducting adaptor that is configured to receive a container containing one or more of samples 2910 .
  • the heat conducting adaptor is disposed on heat conducting block 2912 , and the container containing samples 2910 fits into the heat conducting adaptor.
  • FIGS. 32 C-E show three exemplary configurations of a heat conducting adaptor.
  • An adaptor 3200 is configured with round-bottomed wells.
  • An adaptor 3202 is configured with square-bottom wells.
  • An adaptor 3204 is configured with V-shaped wells.
  • adaptor 3200 can receive a plurality of round-bottom containers, each containing one sample.
  • adaptor 3202 can receive a plurality of square-bottom containers
  • adaptor 3204 can contain a plurality of V-shaped bottom containers.
  • Adaptors 3200 , 3202 , and 3204 can also receive a carrier for a multiplicity of round-bottom containers.
  • An exemplary carrier is a microtitre plate having a plurality of wells, each well containing a sample.
  • heat conducting block 2912 is heated
  • heat conducting adaptors 3200 , 3202 , or 3204 are also heated.
  • the samples contained in the containers that fit within adaptors 3200 , 3202 , or 3204 are also heated.
  • Adaptors 3200 , 3202 , and 3204 can accept standard microplate geometries.
  • FIG. 33 Another embodiment of the assay apparatus of the present invention is shown in FIG. 33.
  • a plurality of heat conducting blocks 2912 is mounted on a rotatable platform or carousel 3306 .
  • the platform can be a translatable platform.
  • Platform or carousel 3306 can be composed of a heat conducting material, such as the material that heat conducting block 2912 is composed of.
  • six heat conducting blocks are shown in FIG. 33, this number is exemplary and it is to be understood that any number of heat conducting blocks can be used.
  • an axle 3308 is rotatably connected to base 3100 .
  • Rotatable platform 3306 is axially mounted to rotate about axle 3308 .
  • Rotation of axle 3308 is controlled by a servo controller 3312 .
  • Servo controller 3312 is controlled by a computer controller 3314 in a manner well known to one of skill in the relevant arts.
  • Computer controller 3314 causes servo controller 3312 to rotate axle 3308 thereby rotating rotatable platform 3306 . In this manner, heat conducting blocks 2912 are sequentially placed under fiber optic probe 3122 .
  • Each of the plurality of heat conducting blocks 2912 can be controlled independently by temperature controller 3162 .
  • the temperature of a first heat conducting block 2912 can be higher or lower than the temperature of a second heat conducting block 2912 .
  • the temperature of a third heat conducting block 2912 can be higher or lower than the temperature of either first or second heat conducting block 2912 .
  • relative movement means 3130 is also used to move sensor armature 3120 in directions 3150 and 3152 so that fiber optic probe 3122 can be moved to detect spectral emission from samples 2910 .
  • a second sensor armature relative movement means 3316 is used to move sensor armature 3120 in directions 3154 and 3156 .
  • the temperature of heat conducting blocks 2912 is controlled by temperature controller 3162 .
  • Temperature controller 3162 is connected to rotatable platform 3306 by connection 3164 to heat conducting blocks 2912 . Under the action of temperature controller 3162 , the temperature of heat conducting blocks 2912 can be increased and decreased.
  • temperature controller 3162 can be configured to adjust the temperature of rotatable platform 3306 . In such a configuration, when rotatable platform 3306 is heated, heat conducting blocks 2912 are also heated.
  • the temperature of each of heat conducting blocks 2912 can be controlled by a circulating water system such as that noted above.
  • excitatory light source 2906 is used to excite samples 2910 .
  • Excitatory light source 2906 is communicatively and operably connected to excitatory light filter 3104 , which is contained within excitatory light filter housing 3160 .
  • Excitatory light filter 3104 filters out all wavelengths of light from excitatory light source 2906 except for the wavelength(s) of light that are desired to be delivered by fiber optic probe 3122 to samples 2910 .
  • An excitatory light filter servo controller 3106 controls the aperture of excitatory light filter 3104 .
  • Excitatory light source 2906 and excitatory light filter servo controller 3106 are communicatively and operatively connected to excitatory light computer controller 3102 .
  • Computer controller 3102 controls the wavelength of excitatory light transmitted to samples 2910 by controlling excitatory light filter servo controller 3106 .
  • Excitatory light 2916 is transmitted through excitatory light input fiber optic cable 3108 to fiber optic probe 3122 for transmission to samples 2912 .
  • Spectral emission 2918 from samples 2910 is received by fiber optic probe 3122 and is transmitted to spectral emission filter 3114 by fiber optic cable 3110 .
  • Spectral emission servo controller 3112 controls spectral emission filter 3114 aperture and thus controls the wavelength of spectral emission that is transmitted to photomultiplier tube 2904 .
  • spectral emission servo controller 3112 is controlled by computer controller 3170 .
  • the assay apparatus of the present invention can detect spectral emission from samples 2910 one sample at a time or simultaneously from a subset of samples 2910 .
  • the term “subset of samples” refers to at least two of samples 2910 .
  • a plurality of excitatory light filters 3104 , excitatory light input fiber optic cables 3108 , emission light output fiber optic cables 3110 , and emission light filters 3114 must be used.
  • the spectral emission signal is transmitted from photomultiplier tube 2904 to computer 2914 .
  • Photomultiplier tube 2904 is communicatively and operatively coupled to computer 2914 by electrical connection 2902 .
  • Connection 2902 is connected to photomultiplier tube 2904 through electrical output 3140 .
  • Computer 2914 functions as a data analysis means for analyzing spectral emission as a function of temperature.
  • FIG. 34 illustrates a top view of the assay apparatus shown in FIG. 33 with a housing 3400 that covers the apparatus.
  • a door 3402 opens to reveal samples 2910 .
  • Door 3402 can be a hinge door that swings open. Alternatively, door 3402 can be a sliding door that slides open.
  • a side view of the assay apparatus shown in FIGS. 33 and 34 is illustrated in FIG. 35.
  • Cover 3400 is disposed on top of base 3100 .
  • Cover 3400 can be made of any suitable material.
  • cover 3400 can be made of plexiglass, fiberglass, or metal.
  • FIG. 36A illustrates a temperature profile 3600 that shows the temperature of heat conducting blocks 2912 as a function of time.
  • Heat conducting blocks 2912 and samples 2910 are heated in a continuous fashion in accordance with temperature profile 3600 .
  • rotatable platform 3306 can be heated along with heat conducting blocks 2912 :
  • temperature profile 3600 is linear, with temperatures ranging from about 25° C. to about 110° C.
  • temperature profile 3600 can be characterized by incremental, stair step increases in temperature, in which heat conducting blocks 2912 and samples 2910 are heated to a predetermined temperature, maintained at that temperature for a predetermined period of time, and than heated to a higher predetermined temperature.
  • temperature can be increased from 0.5° C. to 20° C. per minute.
  • the temperature range from about 25° C. to about 110° C. is disclosed, it is to be understood that the temperature range with which a given target molecule, for example, a protein, is to be heated to generate a thermal denaturation curve can readily be determined by one of ordinary skill in the art.
  • the length of time over which temperature profile 3600 is accomplished will vary, depending on how many samples are to be assayed and on how rapidly the sensor that receives spectral emission 2918 can detect spectral emission 2918 from samples 2910 .
  • an experiment in which each of six heat conducting blocks 2912 holds a total of 96 samples 2910 (for a total of 576 samples), and in which samples are scanned using a fluorescent reader device having a single fiber optic probe, and in which the temperature profile is from 38° C. and 76° C. would take approximately 38 minutes to perform using the apparatus shown in FIG. 33.
  • spectral emission 2918 from each sample 2910 in a first heat conducting block 2912 is received through fiber optic probe 3122 .
  • platform 3306 is rotated to move the next heat conducting block 2912 under fiber optic probe 3122 and spectral emission 2918 from samples 2910 is received by fiber optic probe 3122 . This process is continued until reception of spectral emissions from all samples in all heat conducting blocks 2912 is complete.
  • Spectral emission from samples 2910 on each heat conducting block 2912 can be received one at a time, simultaneously from a subset of samples, simultaneously from one row of samples at a time, or all of the samples at one time.
  • the present invention may be implemented using hardware, software, or a combination thereof, and may be implemented in a computer system or other processing system.
  • a flowchart 3800 for implementation of one embodiment of the present invention is shown in FIG. 38.
  • Flowchart 3800 begins with a start step 3802 .
  • temperature profile 3600 is initiated.
  • temperature controller 3162 causes the temperature of heat conducting block 2912 to increase.
  • a sensor such as fiber optic probe 3122 or CCD camera 3000 is moved over a sample 2910 , row of samples 2910 , or all of samples 2910 .
  • excitatory light is transmitted to sample(s) 2910 using excitatory light source 2906 .
  • spectral emission is received by the sensor from sample(s) 2910 .
  • a decision step 3812 it is determined whether spectral emission 2918 has been received from all of the samples, rows of samples, in one heat conducting block 2912 . If spectral emission 2918 has not been received from all of the samples or rows of samples, the sensor is moved over the next sample or row of samples in a step 3814 . Processing then continues at step 3808 to transmit excitatory light 2916 . Processing then continues to a step 3810 to receive spectral emission 2918 from sample(s) 2910 .
  • spectral emission 2918 has been received from all of samples or rows of samples, processing continues to a decision step 3816 .
  • decision step 3816 it is determined whether spectral emission 2918 has been received from samples in all heat conducting blocks. If not, rotatable platform 3306 is rotated in a step 3818 to place the next heat conducting block 2912 and samples 2910 contained therein under the sensor. Steps 3806 through 3818 are followed until spectral emission 2918 has been received from all of the samples in all of heat conducting blocks 2912 . Processing then continues to a step 3820 , in which temperature profile 3600 is completed and processing ends at a step 3822 .
  • FIG. 39 A flowchart 3900 for implementation of an alternate embodiment of the present invention is shown in FIG. 39.
  • a sensor for simultaneously receiving spectral emission 2918 from all of samples 2910 on heat conducting block 2912 such as CCD camera 3000 , is positioned over heat conducting block 2912 .
  • Flowchart 3900 begins with a start step 3902 .
  • temperature profile 3600 is initiated.
  • temperature controller 3162 causes the temperature of heat conducting block 2912 to increase.
  • excitatory light is transmitted to sample(s) 2910 using excitatory light source 2906 .
  • spectral emission is received by CCD camera 3000 from sample(s) 2910 .
  • a decision step 3910 it is determined whether spectral emission 2918 has been received from all of heat conducting blocks 2912 . If not, rotatable platform 3306 is rotated in a step 3912 to place the next heat conducting block 2912 and samples 2910 contained therein under CCD camera 3000 . Steps 3906 through 3912 are followed until spectral emission 2918 has been received from samples 2910 in all of heat conducting blocks 2912 . Processing then continues to a step 3914 . In step 3914 , temperature profile 3600 is completed and processing ends at a step 3916 .
  • the present invention may be implemented using hardware, software, or a combination thereof, and may be implemented in a computer system or other processing system.
  • An exemplary computer system 3702 is shown in FIG. 37.
  • Computer controllers 3102 , 3142 , 3162 , 3170 , or 3314 can be implemented using one or more computer systems such as computer system 3702 .
  • Computer system 3702 includes one or more processors, such as processor 3704 .
  • Processor 3704 is connected to a communication bus 3706 .
  • Computer system 3702 also includes a main memory 3708 , preferably random access memory (RAM), and can also include a secondary memory 3710 .
  • the secondary memory 3710 can include, for example, a hard disk drive 3712 and/or a removable storage drive 3714 , representing a floppy disk drive, a magnetic tape drive, an optical disk drive, etc.
  • the removable storage drive 3714 reads from and/or writes to a removable storage unit 3716 in a well known manner.
  • Removable storage unit 3716 represents a floppy disk, magnetic tape, optical disk, etc. which is read by and written to by removable storage drive 3714 .
  • the removable storage unit 3716 includes a computer usable storage medium having stored therein computer software and/or data.
  • secondary memory 3710 may include other similar means for allowing computer programs or other instructions to be loaded into computer system 3702 .
  • Such means can include, for example, a removable storage unit 3718 and an interface 3720 .
  • Examples of such can include a program cartridge and cartridge interface (such as that found in video game devices), a removable memory chip (such as an EPROM, or PROM) and associated socket, and other removable storage units 3718 and interfaces 3720 which allow software and data to be transferred from the removable storage unit 3718 to computer system 3702 .
  • Computer system 3702 can also include a communications interface 3722 .
  • Communications interface 3722 allows software and data to be transferred between computer system 3702 and external devices.
  • Examples of communications interface 3722 can include a modem, a network interface (such as an Ethernet card), a communications port, a PCMCIA slot and card, etc.
  • Software and data transferred via communications interface 3722 are in the form of signals 3724 which can be electronic, electromagnetic, optical or other signals capable of being received by communications interface 3722 . These signals 3724 are provided to communications interface via a channel- 3726 .
  • This channel 3726 carries signals 3724 and can be implemented using wire or cable, fiber optics, a phone line, a cellular phone link, an RF link and other communications channels.
  • one example of channel 3726 is electrical connection 2902 that carries signal 3724 of spectral emission 2918 to computer 2914 .
  • computer program medium and “Computer usable medium” are used to generally refer to media such as removable storage device, 3716 and 3718 , a hard disk installed in hard disk drive 3712 , and signals 3724 . These computer program products are means for providing software to computer system 3702 .
  • Computer programs are stored in main memory 3708 and/or secondary memory 3710 . Computer programs can also be received via communications interface 3722 . Such computer programs, when executed, enable the computer system 3702 to perform the features of the present invention as discussed herein. In particular, the computer programs, when executed, enable the processor 3704 to perform the features of the present invention. Accordingly, such computer programs represent controllers of the computer system 3702 .
  • the software may be stored in a computer program product and loaded into computer system 3702 using removable storage drive 3714 , hard drive 3712 or communications interface 3722 .
  • the control logic when executed by the processor 3704 , causes the processor 3704 to perform the functions of the invention as described herein.
  • the invention is implemented primarily in hardware using, for example, hardware components such as application specific integrated circuits (ASICs).
  • ASICs application specific integrated circuits
  • the invention is implemented using a combination of both hardware and software.
  • the assay apparatus of the present invention is particularly suited for carrying out the methods of the present invention.
  • samples are placed in a heat conducting block, heated according to a predetermined temperature profile, stimulated with an excitatory wavelength of light, and the spectral emission from the samples is detected while the samples are being heated in accordance with the pre-determined temperature profile.
  • the assay apparatus of the present invention is not limited to use with the methods of the present invention or limited to conducting assays on biological polymers, proteins, or nucleic acids.
  • the assay apparatus of the present invention can be used to incubate samples to a predetermined temperature.
  • the assay apparatus of the present invention can be used to perform polymerase chain reaction, thermal cycling steps for any purpose, assaying thermal stability of a compound, such as a drug, to determine conditions that stabilize a compound, or to determine conditions that facilitate crystallization of a compound.
  • K i 's for these compounds ranged from 7.7 nM for 3dp-4026 to 20.0 ⁇ M for 3dp-3811.
  • a stock human ⁇ -thrombin solution (1.56 mg/mL) from Enzyme Research Labs was first diluted to 0.5 mg/mL (11 ⁇ M) with 50 mM Hepes, pH 7.5, 0.1 M NaCl (assay buffer, unless mentioned otherwise), and stored on ice.
  • the five ligands (recrystallized solids characterized by mass spectrometry and NMR) were accurately weighed out to be 1.5 to 2.0 mg and dissolved in 1.0 mL of 100% DMSO so that the concentration was between 1.8 and 3.8 mM.
  • a 96 well V-bottom Costar microplate was then set up such that 100 ⁇ L of the 11 ⁇ M human ⁇ -thrombin solution was pipetted into wells A1 through A6. This was followed by the addition of 2 ⁇ L of 3dp-3811 into well A2, 2 ⁇ L of 3dp-3959 into well A3, 2 ⁇ L of 3dp-4077 into well A4, 2 ⁇ L of 3dp-4076 into well A5, 2 ⁇ L of 3 dp-4026 into well A6, and 2 ⁇ L of 100% DMSO into control well A1. The contents were mixed by repeated uptake and discharge using a 100 ⁇ L pipette tip. Finally, one drop of mineral oil (Sigma, St.
  • the microplate was then placed on heating block 4 of a RoboCycler Gradient 96 Temperature Cycler (Stratagene, La Jolla, Calif.), set at 25° C., for 1 minute.
  • the plate was then placed into a SPECTRAmaxTM 250 spectrophotometer (set to 30° C.) and the absorbance at 350 nm was measured for each sample. This reading served as the blank or reference from which all the other readings at higher temperatures were compared.
  • the assay was initiated by setting heating block 1 to 38° C., programming the temperature cycler to move the microplate to heating block 1, and keeping the microplate there for 3 minutes.
  • the plate was moved to the 25° C. block (Block 4) for 30 seconds, inserted in the spectrophotometer, and absorbance was read at 350 nm.
  • the microplate was then put back into the temperature cycler and was moved to heating block 2, which had been pre-equilibrated at 40° C. After 3 minutes at 40° C., the plate was returned to 25° C. (on block 4) for 30 seconds, and was returned to the spectrophotometer for a measurement of absorbance at 350 nm. This process was repeated 18 more times until the temperature had been raised to 76° C. in 2° C. increments. After subtraction of the blank absorbance (A 350 at 25° C.), turbidity, reflected in the absorbance value, was plotted as a function of temperature. The thermal denaturation curves for this experiment are shown in FIG. 1.
  • Assays for ligands that bind to the heparin binding site of human ⁇ -thrombin are more difficult to perform than assays for ligands that bind to the active site of human ⁇ -thrombin.
  • At the heparin binding site no substrate is hydrolyzed, so no spectrophotometric signal can be amplified for instrumental detection.
  • Heparin activity is usually estimated in biological clotting time assays.
  • heparin binding affinity for human ⁇ -thrombin can be determined I 0 by laboriously conducting 15 to 20 single point assays, in which the concentration of low MW heparin is varied over two logs, and monitoring the quenching of the fluorescent probe, p-aminobenzamidine, bound to the active site of human ⁇ -thrombin (Olson, S. T. et al., J. Biol. Chem . 266:6342-6352 (1991)).
  • heparin binding to human ⁇ -thrombin represents the kind of challenge encountered with the vast majority of non-enzyme receptor/ligand binding events, which are commonly observed for hormone/receptor interactions, repressor/DNA interactions, neurotransmitter/receptor interactions, etc.
  • Several heparin-like sulfated oligosaccharides and sulfated naphthalene compounds were assayed by the microplate thermal shift assay. Using the thermal shift assay, it was possible to use a single compound per well to quickly rank the compounds in order of increasing binding affinity, with K d 's ranging over three orders of magnitude (see Table 4).
  • the second therapeutic receptor tested in the microplate thermal shift assay was acidic fibroblast growth factor (aFGF), a growth factor that plays a key role in angiogenesis (Folkman, J. et al., J. Biol. Chem. 267:10931-10934 (1992)).
  • a synthetic gene for this protein was purchased from R&D Systems (Minneapolis, Minn.), and was cloned and expressed in E. coli using methods similar to those described for basic fibroblast growth factor (bFGF) (Thompson, L. D. et al., Biochemistry 33:3831-3840 (1994); Pantoliano, M. W.
  • aFGF Recombinant aFGF was then purified by heparin-sepharose affinity chromatography as described (Thompson, L. D. et al., Biochemistry 33:3831-3840 (1994)).
  • aFGF is also known to bind heparin/heparan, which is a cofactor for mitogenic activity.
  • Heparin-like molecules, such as pentosan PSO 4 and suramin inhibit the growth factor's biological activity.
  • a microplate thermal assay of these compounds was set up in a way similar to that described above for human ⁇ -thrombin.
  • the change in turbidity, as a function of temperature, for each of the ligands suramin, heparin 5000, and pentosan PSO 4 is shown in FIG. 2.
  • the results are summarized in Table 5.
  • the affinity constants covered a fairly broad range of binding affinities, with pentosan PSO 4 showing the highest affinity.
  • the order of ligand binding affinity of pentosan PSO 4 , heparin 5000 and suramin paralleled that found for bFGF, as measured using isothermal titrating calorimetry (Pantoliano, M. W. et al., Biochemistry 33:10229-10248 (1994)).
  • the lack of alternatively measured binding affinities for these compounds probably attests to the difficulty of making these measurements using assays which do not monitor physical, temperature-dependent changes.
  • the microplate thermal shift assay was used to assess ligands for binding to the heparin binding site of basic fibroblast growth factor (bFGF).
  • bFGF basic fibroblast growth factor
  • the gene for bFGF was purchased from R&D Systems and was cloned and expressed in E. coli as previously described (Thompson, L. D. et al., Biochemistry 33:3831-3840 (1994); Pantoliano, M. W. et al., Biochemistry 33:10229-10248 (1994); Springer, B. A. et al., J. Biol. Chem. 269:26879-26884 (1994)).
  • fluorescence thermal shift assay was used to assess ligand binding to human ⁇ -thrombin.
  • the fluorescence emission spectra of many fluorophores are sensitive to the polarity of their surrounding environment and therefore are effective probes of phase transitions for proteins (i.e., from the native to the unfolded phase).
  • the most studied example of these environment dependent fluorophores is 8-anilinonaphthalene-1-sulfonate (1,8-ANS), for which it has been observed that the emission spectrum shifts to shorter wavelengths (blue shifts) as the solvent polarity decreases.
  • These blue shifts are usually accompanied by an increase in the fluorescence quantum yield of the fluorophore. In the case of ANS, the quantum yield is 0.002 in water and increases to 0.4 when ANS is bound to serum albumin.
  • ANS was used as a fluorescence probe molecule to monitor protein denaturation.
  • the final concentration of human ⁇ -thrombin was 0.5 ⁇ M, which is 20-fold more dilute than the concentrations used in the turbidity assays. This concentration of human ⁇ -thrombin is in the range used for the kinetic screening assays.
  • ANS was excited with light at a wavelength of 360 nm.
  • the fluorescence emission was measured at 460 nm using a CytoFluor II fluorescence microplate reader (PerSeptive Biosystems, Framingham, Mass.).
  • the temperature was ramped up as described above for the turbidity assays (see Example 1).
  • the plot of fluorescence as a function of temperature is shown in FIG. 3 for human ⁇ -thrombin alone, and for the 3dp-4026/human ⁇ -thrombin complex.
  • the denaturation transition for human ⁇ -thrombin was clearly observed at 57° C., a temperature which is only slightly higher than that observed in the turbidity experiment.
  • the denaturation transition signal is much cleaner than the signal in the turbidity assays.
  • higher concentrations of protein led to precipitation of denatured protein. Precipitated protein contributed to the noisy signal.
  • D(II) FGFR1 is a 124 residue domain which is responsible for most of the free energy of binding for bFGF.
  • D(II) FGFR1 was cloned and expressed in E. coli .
  • Recombinant D(II) FGFR1 was renatured from inclusion bodies essentially as described (Wetmore, D. R. et al., Proc. Soc. Mtg., San Diego, Calif.
  • D(II) FGFR1 was further purified on a heparin-sepharose column (Kan, M. et al., Science 259:1918-1921 (1993); Pantoliano, M. W. et al., Biochemistry 33:10229-10248 (1994)). Purity was >95%, as judged by SDS-PAGE.
  • the D(II) FGFR1 protein was concentrated to 12 mg/mL ( ⁇ 1 mM) and stored at 4° C.
  • the D(II) FGFR1 protein was dissolved in an ANS solution to a concentration of 1.0 mg/mL (70 ⁇ M).
  • the quantum yield for ANS bound to the denatured form of D(II) FGFR1 was lower than the quantum yield for ANS bound to human ⁇ -thrombin. Because ANS fluorescence is very environment dependent (see Lakowicz, I. R., Principles of Fluorescence Spectroscopy, Plenum Press, New York (1983)), the quantum yield observed for the denaturation of different proteins will vary. For D(II) FGFR1, the signal for the turbidity version of the assay, however, was nearly undetectable.
  • Factor D is an essential serine protease involved in the activation of the alternative pathway of the complement system, the major effector system of the host defense against invading pathogens.
  • Factor D was purified from the urine of a patient with Fanconi's syndrome (Narayana et al., J. Mol. Biol . 235:695-708 (1994)) and diluted to 4 ⁇ M in assay buffer (50 mM Hepes, pH 7.5, 0.1 M NaCl). The assay volume was 10 ⁇ L and the concentration of 1,8-ANS was 100 ⁇ M.
  • the experiment was carried out using 15 ⁇ L round bottom dimple plates (an 8 ⁇ 12 well array).
  • the protein was heated in two 30 degree increments between 42° C. to 62° C., using a RobocyclerTM temperature cycler. After each heating step, and prior to fluorescence scanning using the CytoFluor IITM fluorescence plate reader the sample was cooled to 25° C. (see Example 1).
  • the non-linear least squares curve fitting and other data analysis were performed as described for FIG. 3.
  • the results of the microplate thermal shift assay of Factor D is shown in FIG. 5 and reveal a thermal unfolding transition that occurs near 324 K (51° C.) for the unliganded form of the protein. No reversible ligands of significant affinity are known for Factor D.
  • the results in FIG. 5 show that the microplate thermal shift assay can be used to screen a library of compounds for Factor D ligands.
  • the results in FIG. 5 also show that the microplate thermal shift assay is generally
  • Human Factor Xa a key enzyme in the blood clotting coagulation pathway, was chosen as yet another test of the cross target utility of the microplate thermal shift assay.
  • Factor Xa was purchased from Enzyme research Labs (South Bend, Ind.) and diluted to 1.4 ⁇ M in assay buffer (50 mM Hepes, pH 7.5, 0.1 M NaCl). The assay volume was 100 ⁇ L and the concentration of 1,8-ANS was 100 ⁇ M.
  • the protein was heated in two degree increments between 50° C. to 80° C. using a RobocyclerTM temperature cycler. After each heating step, prior to fluorescence scanning using the CytoFluor IITM fluorescence plate reader, the sample was cooled to 25° C.
  • FIG. 6 The results of a microplate thermal shift assay of Factor Xa is shown in FIG. 6. A thermal unfolding transition was observed at 338K (65° C.). Data analysis was described as described for FIG. 3. The results in FIG. 6 show that the microplate thermal shift assay of protein stability is generally applicable to any target molecule.
  • a miniaturzed form of the microplate thermal shift assay was developed to minimize the amount of valuable therapeutic protein and ligands required for the assay.
  • the assay volume was decreased from 100 ⁇ L to 50 ⁇ L without adversely affecting the fluorescent signal.
  • the assay volume was reduced further by a factor of ten, to 5 ⁇ L, favorable results were obtained for human ⁇ -thrombin.
  • the human ⁇ -thrombin unfolding transition could be easily observed at its usual T m .
  • an active site inhibitor was observed to shift the T m of the unfolding transition by 8.3° K to yield an estimate of the K d of 15 nM at the T m .
  • T m 332.2° K (midpoint of the unfolding transition in the absence of a ligand)
  • ⁇ C pu 2.0 kcal/mol (estimated change in heat capacity of unfolding for human ⁇ -thrombin)
  • the measurements shown in FIG. 7 were obtained using the CytoFluor II fluorescence plate reader (PerSeptive Biosystems, Framingham, Mass.). In the experiment, the excitation wavelength of light was 360 nm and the emission was measured at 460 nm.
  • the microplates employed for this miniaturized assay were either the conventional polycarbonate V-bottom 96 well plate (Stratagene, or Costar) or polycarbonate plates that contain 15 ⁇ L dimples in an 8 ⁇ 12 array (Costar plate lids). In the reaction, the concentration of human ⁇ -thrombin was ⁇ M in assay buffer (50 mM Hepes, pH 7.5, 0.1 M NaCl).
  • the assay volume was 5 ⁇ L and the concentration of 1,8-ANS was 100 ⁇ M.
  • the protein was heated in two degree increments between 44° C. to 64°C. using a RobocyclerTM temperature cycler. After each heating step, and prior to fluorescence scanning using the CytoFluor IITM fluorescence plate reader the sample was cooled to 25° C. for 30 seconds (see Example 1). The non-linear least squares curve fitting and other data analysis were performed as described for FIG. 3.
  • Recombinant D(II) FGFR1 was purified from inclusion bodies and purified by affinity chromatography on heparin sepharose.
  • a stock solution of D(II) FGFR1 (15 mg/ml; 1.1 mM) was diluted to 50 ⁇ M in assay buffer (50 mM Hepes, pH 7.5, 0.1 M NaCl).
  • the assay volume was 10 ⁇ L and the concentration of 1,8-ANS was 250 ⁇ M.
  • the unfolding transition in the absence of ligands was found to be about 312 K (39° C.) as shown in FIG. 8.
  • U-PA human urokinase-type plasminogen activator
  • U-PA enzymatically converts plasminogen into the active protease plasmin.
  • U-PA is involved in tissue remodeling, cellular migration and metastases.
  • the gene for u-PA was obtained from ATCC (Rockville, Md.) and modified to appropriately express active enzyme in E. coli .
  • u-PA was cloned, overexpressed in E. coli , and purified using procedures similar to those described by Winkler et al. ( Biochemistry 25:4041-4045 (1986)).
  • CMK active site inhibitor glu-gly-arg-chloromethylketone
  • the experiment was performed in the miniaturized format in 5 ⁇ L well volume.
  • One ⁇ L of concentrated CMK-u-PA (13 g/L, 371.4 ⁇ M) was added to 4 ⁇ L of 62.5 mM MOPS, pH 7, 125 mM NaCl, and 250 ⁇ M 1,8-ANS, in multiple wells of a 96-well polycarbonate V-bottom microtiter plate.
  • a thermal denaturation curve was generated as previously described for thrombin, aFGF, D(II)FGFR1, Factor D, and Factor Xa, by incremental heating of the microplate followed by a fluorescence reading after each temperature increase. Analysis and non-linear least squares fitting of the data for this experiment show that the T m for CMK-u-PA under these conditions is 81° C., which is considerably higher than that seen for thrombin, aFGF, D(II)FGFR1, Factor D, and Factor Xa (55,44,40, 51, 55, and 65° C., respectively).
  • This experiment demonstrates the utility of the current invention in determining the T m for relatively thermostable proteins or proteins stabilized by the high affinity binding of ligand(s) and further demonstrates the ability to perform such an experiment in a miniaturized format.
  • a stock thrombin solution was diluted to 1 ⁇ M in 50 mM Hepes, pH 7.5, 0.1 M NaCl and 100 ⁇ M 1,8-ANS.
  • An electronic multi-channel pipettor was used to dispense either 2 ⁇ L or 5 ⁇ L of diluted thrombin solution into wells of a 96-well polycarbonate microtiter plat.
  • the plate was subjected to 3 minutes of heating in a thermal block capable of establishing a temperature gradient across the microplate, followed by 30 seconds cooling to 25° C., and subsequent reading in the CytoFluor II fluorescence plate reader. Data were analyzed by non-linear least squares fitting and plotted as shown in FIGS. 10 and 11. Each curve represents a replicate experiment.
  • the assay volume was reduced to 2 ⁇ L, as shown for human ⁇ -thrombin (1.0 ⁇ M) in FIG. 11.
  • Reproducible pipetting of 2 ⁇ L in a 96 well array requires the employment of specialized pipetting tools such as the multi-channel pipettor available from Matrix Technologies Corp. (Lowell, Mass.) which has ⁇ 2.0% or 0.15 ⁇ L precision and ⁇ 2.5% or 0.15 ⁇ L accuracy for volumes 0.5 to 12.5 ⁇ L.
  • Results of a single temperature assay are shown in FIG. 12.
  • the compounds 3DP-3811, 3DP-3959, 3DP-4076, and 3DP-4660 bind to the active site of human ⁇ -thrombin.
  • the K i 's (enzymatically determined) of these four compounds for human ⁇ -thrombin are of 20,000 nM, 250 nM, 25 nM, and 8 nM, respectively.
  • Each of these four compounds were equilibrated with human ⁇ -thrombin in separate 5 ⁇ l assay volumes in a 96 well plate. The final ligand concentration was 50 ⁇ M.
  • the intrinsic Trp fluorescence of human ⁇ -thrombin was assayed in a microplate thermal shift assay. 100 ⁇ L samples contained 2 ⁇ M human ⁇ -thrombin. The samples were exposed to light from a Xenon-Arc lamp at 280 nm. Emission was detected at 350 nm using the BioLumin 960 (Molecular Dynamics). Temperature cycling, between 44° C. and 66° C., was performed as described in previous examples. The results of the assay are shown in FIGS. 13 and 14. A small increase in fluorescence emission was observed at 350 nm with increasing temperature. However, this increase in fluorescence emission was barely detectable above the level of fluorescence in the blank wells that contained no protein (FIG. 13).
  • the thermal shift assay can be used for the screening of ligands for binding to single sites on target proteins.
  • the microplate thermal shift assay In light of the underlying physical principles upon which the microplate thermal shift assay is based, the near additivity of the free energy of ligand binding and protein unfolding, it is possible to employ the microplate thermal shift assay for analyzing multi-ligand binding interactions with a target protein. If the free energy of binding of different ligands binding to the same protein are nearly additive, then one can analyze multi-ligand binding systems, whether the ligands bind in a cooperative (positive) fashion or a non-cooperative (negative) fashion.
  • Human ⁇ -thrombin it has at least four different ligand binding sites: (1) the catalytic binding site; (2) the fibrin binding site (exosite I); (3) the heparin binding site (exosite II); and (4) the Na + binding site, located ⁇ 15 ⁇ from the catalytic site.
  • a stock thrombin solution was diluted to 1 ⁇ M in 50 mM Hepes, pH 7.5, 0.1 M NaCl, 1 mM CaCl 2 , and 100 ⁇ M 1,8-ANS.
  • Each thrombin ligand was included singly and in various combinations to 1 ⁇ M thrombin solutions at final concentrations of 50 ⁇ M each, except for heparin 5000, which was 209 ⁇ M.
  • 100 ⁇ L of thrombin or thrombin/ligand(s) solution was dispensed into wells of a 96-well V-bottom polycarbonate microtiter plate.
  • the plate was subjected to 3 minutes of heating in a thermal block capable of establishing a temperature gradient across the microplate, followed by 30 seconds cooling at 25° C., and subsequent reading in a fluorescence plate reader. Data were analyzed by non-linear least squares fitting.
  • FIGS. 15 and 16 The results of these individual binding reactions are shown in FIGS. 15 and 16.
  • the rank order of binding affinity was 3DP-4660 >Hirugen >heparin 5000, corresponding to K d values of 15 nM, 185 nM and 3434 nM, respectively, for the ligands binding at each T m (see Equation (4)).
  • FIG. 15, FIG. 16, Table 7 illustrate the following advantages of using the microplate thermal shift assay to perform multi-variable analyses.
  • the same microplate thermal shift assay can be used to simultaneously detect the binding of multiple ligands at multiple binding sites in a target protein.
  • the microplate thermal shift assay can be used to detect the same ligand binding to two or more sites in a therapeutic target.
  • the microplate thermal shift assay affords the detection of cooperativity in ligand binding. Information about ligand binding cooperativity can be collected and analyzed very quickly. Thus, multi-ligand binding experiments that would take months to perform using alternative technologies take only hours to perform using the microplate thermal shift assay.
  • the microplate thermal shift assay was used, with four different fluorophores, to simultaneously screen the effects of multiple pH values, sodium chloride concentrations, and reduction-oxidation compounds on human ⁇ -thrombin stability.
  • Thrombin solution was diluted to 1 ⁇ M in 50 mM Hepes, pH 7.5, NaCl at either 0.1 M or 0.5 M, 10 mM EDTA, 10 mM CaCl 2 , 10 mM dithiothreitol, 10 1 mM CaCl 2 , and 100 ⁇ M 1,8-ANS, 10% (v/v) glycerol, or 0.1% (w/v) polyethylene glycol (PEG) 6000. Reaction volume was 100 ⁇ L.
  • FIGS. 17 A-D summarize the stability data collected in a single 96 well plate for human ⁇ -thrombin.
  • the fluorophore is 1,8-ANS.
  • the fluorophore is 2,6-ANS.
  • the fluorophore is 2,6-TNS.
  • the fluorophore is bis-ANS.
  • the results in FIGS. 17 A-D show a pH optimum of about 7.0 and an increase in stability with increasing NaCl concentration. A ⁇ T m of about 12° C. was observed when the NaCl concentration was increased from 0 to 0.5 M.
  • FIG. 17A the fluorophore is 1,8-ANS.
  • the fluorophore is 2,6-ANS.
  • the fluorophore is 2,6-TNS.
  • the fluorophore is bis-ANS.
  • the results in FIGS. 17 A-D show a pH optimum of about 7.0 and an increase in stability with increasing NaCl concentration. A ⁇ T m of about 12° C
  • the additional stabilization that occurs at a NaCl concentration of greater than 0.10 M may come from additional Na + and/or Cl ⁇ binding events summed over the entire structure of human ⁇ -thrombin.
  • the source of this further stabilization may come from less specific salting out effect that is usually observed at 0.5 to 2 M NaCl and is due to the preferential hydration of proteins induced by salts (Timasheff & Arakawa, In: Protein Structure, A Practical Approach , T. E. Creighton, ed., IRL Press, Oxford, UK (1989), pp. 331-354)).
  • the microplate thermal shift assay was used to simultaneously screen the effects of multiple biochemical conditions on D(II) FGF receptor 1 stability.
  • the assays were performed by mixing 1 ⁇ L of D(II) FGFR1 (from a 500 ⁇ M concentrated stock in 50 mM HEPES pH 7.5) with 4 ⁇ L of each biochemical condition in wells of a 96-well polycarbonate microtiter plate. Final protein concentration after mixing was 100 ⁇ M and final. 1,8-ANS concentration was 200 ⁇ M.
  • Biochemical conditions were tested as follows: The pH's tested were 5 (Na acetate), 6 (MES), 7 (MOPS), 8 (HEPES), and 9 (CHES), with final buffer concentrations of 50 mM.
  • the salt concentrations tested were 0.1 or 0.5 M NaCl. Additives were tested in 50 mM MOPS, pH 7, 0.1 M NaCl, at final concentrations of 1 mM (EDTA, dithiothreitol), 10 mM (CaCl 2 , MgCl 2 , MgSO 4 , NiSO 4 ), 50 mM (arginine), 100 mM (NH 4 ) 2 SO 4 , LiSO 4 , Na 2 SO 4 , ZnSO 4 ), 5% w/v (polyethylene glycol 6000), and 10% v/v glycerol.
  • EDTA dithiothreitol
  • 10 mM CaCl 2 , MgCl 2 , MgSO 4 , NiSO 4
  • 50 mM (arginine) 100 mM (NH 4 ) 2 SO 4 , LiSO 4 , Na 2 SO 4 , ZnSO 4 ), 5% w/v (polyethylene glycol
  • FIGS. 19-24 The results of these multi-variable experiments are shown in FIGS. 19-24.
  • stability increased with increasing NaCl concentration.
  • a ⁇ T m of about 5° C. was observed as NaCl concentration was increased from 0.1 to 0.5 M.
  • both MgSO 4 and arginine stabilized the protein.
  • 10% glycerol stabilized the protein.
  • salts of the Hofmeister series such as Li 2 SO 4 , Na 2 SO, 4 (NH 4 ) 2 SO 4 and Mg 2 SO 4 all had stabilizing effects (FIG. 21).
  • dithiothreitol destabililzed the protein.
  • the microplate thermal shift assay was used to simultaneously screen the effects of multiple biochemical conditions on human urokinase stability. This experiment was performed by mixing 1 ⁇ L of urokinase (from a 371 5M concentrated stock in 20 mM Tris pH 8) with 4 ⁇ L of each biochemical condition in wells of a 96-well polycarbonate microtiter plate. Final protein concentration after mixing was 74 ⁇ M and final 1,8-ANS concentration was 200 ⁇ M. Biochemical conditions were tested as follows: The pH's tested were 5 (acetate), 6 (MES), 7 (MOPS), 8 (HEPES), and 9 (CHES) with final buffer concentrations of 50 mM. The salt concentrations tested were 0.1 or 0.5 M NaCl. Glycerol was tested at 10% v/v in 50 mM MOPS, pH 7, 0.1 M NaCl.
  • FIGS. 17-25 illustrate the advantage of using the microplate thermal shift assay to simultaneously screen for multi-variable biochemical conditions that optimize protein stability.
  • the methods and apparatus of the present invention one can rapidly screen large arrays of biochemical conditions for conditions that influence the stability of proteins.
  • the present invention can be used to rapidly identify biochemical conditions that optimize protein shelf-life.
  • FIG. 28 shows the results of microplate thermal shift assays of using each of four fluorescence probe molecules: bis-ANS, 2,6-TNS, 1,8-TNS, and 2,6-ANS.
  • Thrombin solution was diluted to 1 ⁇ M in 50 mM Hepes, pH 7.5, and 0.1 M NaCl.
  • a Gel Documentation and Analysis System (Alpha Innotech Corp., San Leandro, Calif.) was used to perform a microplate thermal shift assay.
  • This system uses a CCD camera to detect fluorescence emission from stained gels, dot blot assays, and 96 well plates.
  • the excitatory light source was a long wavelength UV trans-illumination box located directly below the CCD camera.
  • the 96 well plate to be assayed was placed on the trans-illumination box within the focal viewing area of the CCD camera (21 ⁇ 26 cm).
  • a 2 ⁇ M solution of human ⁇ -thrombin was prepared in 50 mM Hepes, pH 7.5, 0.1 M NaCl by diluting a 34 ⁇ M stock solution (1:17) of purified human ⁇ -thrombin (Enzyme Research Labs, Madison, Wis.).
  • the human ⁇ -thrombin solution also contained 100 ⁇ M 1,8-ANS.
  • 100 ⁇ L of the human ⁇ -thrombin-1,8-ANS solution was aliquoted into each of twelve wells of a single row (row A) of a V-bottom polycarbonate microplate (Costar).
  • a gradient block (RoboCyclerTM, Stratagene) was used to heat the twelve samples, from 44 to 66° C., across the rows of the microplate. i.e. a temperature gradient of 2° C. per well was established. Thus, well A1 was at 66° C. and well A12 was at 44° C.
  • the control solution that contained 100 ⁇ M 1,8 ANS in the same buffer (no protein) was placed in each of wells B1 to B 12. After adding a drop of mineral oil to each well to prevent evaporation, the plate was heated on the gradient block for 3 min. The contents of each well were then allowed to reach room temperature and transferred to a flat bottom microplate.
  • FIG. 28 shows the results of microplate thermal shift assays of using each of four fluorescence probe molecules: bis-ANS, 2,6-TNS, 1,8-TNS, and 2,6-ANS.
  • Thrombin solution was diluted to 1 ⁇ M in 50 mM Hepes, pH 7.5, and 0.1 M NaCl.
  • a Gel Documentation and Analysis System (Alpha Innotech Corp., San Leandro, Calif.) was used to perform a microplate thermal shift assay.
  • This system uses a CCD camera to detect fluorescence emission from stained gels, dot blot assays, and 96 well plates.
  • the excitatory light source was a long wavelength UV trans-illumination box located directly below the CCD camera.
  • the 96 well plate to be assayed was placed on the trans-illumination box within the focal viewing area of the CCD camera (21 ⁇ 26 cm).
  • a 2 ⁇ M solution of human ⁇ -thrombin was prepared in 50 mM Hepes, pH 7.5, 0.1 M NaCl by diluting a 34 ⁇ M stock solution (1:17) of purified human ⁇ -thrombin (Enzyme Research Labs, Madison, Wis.).
  • the human ⁇ -thrombin solution also contained 100 ⁇ M 1,8-ANS.
  • 100 ⁇ L of the human ⁇ -thrombin-1,8-ANS solution was aliquoted into each of twelve wells of a single row (row A) of a V-bottom polycarbonate microplate (Costar).
  • a gradient block (RoboCyclerTM, Stratagene) was used to heat the twelve samples, from 44 to 66° C., across the rows of the microplate. i.e. a temperature gradient of 2° C. per well was established. Thus, well A1 was at 66° C. and well A12 was at 44° C.
  • the control solution that contained 100 ⁇ M 1,8 ANS in the same buffer (no protein) was placed in each of wells B1 to B12. After adding a drop of mineral oil to each well to prevent evaporation, the plate was heated on the gradient block for 3 min. The contents of each well were then allowed to reach room temperature and transferred to a flat bottom microplate.
  • the V-bottom well microplate image is shown in FIG. 41A.
  • the dimple plate image is shown in FIG. 41B.
  • the results obtained from the plate in FIG. 41A is shown in FIG. 42.
  • the results in FIG. 42 show that data obtained using a CCD camera compare very well with data obtained using a fluorescence plate reader that employs a photo-multiplier tube (PMT) for fluorescence detection.
  • PMT photo-multiplier tube
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US09/801,676 US6849458B2 (en) 1996-05-09 2001-03-09 Microplate thermal shift assay apparatus for ligand development and multi-variable protein chemistry optimization
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US6214293B1 (en) 2001-04-10
US6291191B1 (en) 2001-09-18
AU3205097A (en) 1997-11-26
JP2000511629A (ja) 2000-09-05
US6303322B1 (en) 2001-10-16
US20020114734A1 (en) 2002-08-22
HUP9902418A2 (hu) 1999-11-29
US6268218B1 (en) 2001-07-31
EP0914608A1 (en) 1999-05-12
KR20000011069A (ko) 2000-02-25
US6020141A (en) 2000-02-01
NZ332754A (en) 2000-07-28
US6036920A (en) 2000-03-14
WO1997042500A1 (en) 1997-11-13
HUP9902418A3 (en) 2001-10-29
CA2253587A1 (en) 1997-11-13
US6232085B1 (en) 2001-05-15
US6291192B1 (en) 2001-09-18
US6849458B2 (en) 2005-02-01
CA2253587C (en) 2008-01-29
US6268158B1 (en) 2001-07-31
US20030203497A1 (en) 2003-10-30
AU741049B2 (en) 2001-11-22

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