Classifications

• • 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
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/536—Immunoassay; Biospecific binding assay; Materials therefor with immune complex formed in liquid phase
  • G01N33/542—Immunoassay; Biospecific binding assay; Materials therefor with immune complex formed in liquid phase with steric inhibition or signal modification, e.g. fluorescent quenching
• • 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
  • C12Q1/34—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase
  • C12Q1/37—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase involving peptidase or proteinase
• • 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
  • C12Q1/48—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase
• • 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
  • C12Q1/48—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase
  • C12Q1/485—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving transferase involving kinase

Definitions

• the present invention relates to methods and tools making it possible to measure post-translational modifications of peptides or proteins in a cell environment.
• a biologically active compound will bind to a molecule involved in a cell mechanism, and will modify its behaviour: such compounds can therefore be detected either by measuring their binding to said molecule involved in a cell mechanism, either by measuring the activation or the inhibition of the considered cell mechanism, in the presence or absence of the compound to be tested.
• modifications of the cell proteins involve enzymes which will modify proteins in the cell.
• modifications of the cell proteins are called post-translational modifications and involve the modification of the skeletal structure of the polypeptide originating from the ribosomal translation by adding or cutting chemical groups, changing the three- dimensional structure or cutting the protein chain.
• modifications include the addition of phosphate (phosphorylation), ADP ribosyl (ADP-ribosylation), a methyl (methylation) or acetyl (acetylation) group, carbohydrate (glycosylation), fatty acid (prenylation), ubiquitin (ubiquitination), SUMO (Sumoylation) or proteolytic cutting of the protein (proteolysis).
• post- translational modifications include hydroxylation, myristoylation, palmitylation, neddylation, iodation, sulphation.
• a certain number of post-translational modifications do not involve enzymes: this is the case with nitration and glutathionylation.
• post-translational modifications are key elements which make it possible to modulate the function of the proteins and hence their role in the cell mechanisms. These post-translational modifications affect the majority of the eukaryotic proteins. They make it possible for the cell, starting from a single gene, to produce several effectors depending on the modifications made to the protein skeletal structure.
• the post-translational modifications determine the state of activation of an enzyme or of a protein, its intracellular location and/or its excretion, the interactions that it can have, its stability and its degradation. These mechanisms are very finely regulated, since they allow the cell to modify its behaviour and adapt to its environment. Frequently, the deregulation of one or more effectors responsible for the post-translational modifications leads to pathological states of the organism.
• a specific probe i.e. capable of distinguishing the modified polypeptide from the non-modified polypeptide
• This approach is very widely used in the field of potential drug screening.
• the methods differ mainly in the method for the detection and/or the technology which makes it possible to demonstrate the fixing of the specific probe to the modified polypeptide.
• the presence in the measurement medium of high concentrations of group donor compounds prevents the detection of inhibitor compounds acting by competition mechanisms.
• the enzyme added to the measurement medium is in general totally active, which is often very far from the physiological reality. In fact, within the cell only a part of the enzyme molecules are activated, or there are even different populations of molecules activated to different degrees.
• the biochemical assays of the prior art do not make it possible to work on these different populations to the extent that they are not implemented under physiological conditions. For the same reason, they no longer make it possible to identify allosteric modulators of these enzymes.
• the in vivo labelling of the target proteins of the post-translational modification involves providing the cells with a co-factor carrying a group which is transferred to the target protein, this group being radiolabeled or more generally marked with a label such as, for example, ADP, Acetyl, GIcNAc, Methyl, Phosphate, Farnesyl, Geranyl, Ubiquitin,
• the modified proteins are then analyzed by electrophoresis or chromatography and autoradiography.
• the specificity of this approach can be increased either by immunoblotting (Western blot), or by including an immunoprecipitation prior to the electrophoresis.
• two-dimensional electrophoresis improves the discrimination between the proteins by separating them not only according to criteria of molecular weight but also by charge.
• Mass spectrometry makes it possible to separate protein fragments according to their mass and their charge, from a complex mixture.
• a post- translational modification increases the mass of a protein sequence. For example: + 80 Da for a phosphorylation, + 42 Da for an acetylation, + 14 Da for a methylation, + 204 Da for a farnesylation, + > 800 Da for an N-bonded glycosylation, + 203 Da or + >800 Da for an O-bonded glycosylation, + 1 kDa for a ubiquitination.
• This technology does not require previous labelling of the target proteins. However the complex mixture of proteins must be fragmented by proteolytic digestion (in general tryptic) before analysis.
• the study by mass spectrometry is often preceded by an enrichment of the modified proteins, using probes specific to post-translational modification.
• the analysis is also sometimes preceded by an electrophoretic separation or microcapillary high pressure liquid chromatography ( ⁇ HPLC).
• Two protein mixtures originating from the same cells taken in different states, are labelled using biochemical probes.
• One of the probes is synthesized with light isotopes of the atoms, the other with heavy isotopes.
• the samples are mixed, then fragmented with trypsin, and enriched on an affinity column.
• the analysis is then carried out by separating the fragments by mass spectrometry. The quantity of a fragment can thus be compared according to the different states of the cell.
• a specific probe i.e. capable of distinguishing the modified protein from the non-modified protein
• antibody lectin, specific protein etc.
• Numerous techniques are based on the use of antibodies for detecting and quantifying the post-translational modifications.
• the modified protein is detected by a probe specific to post-translational modification previously coupled with a development system (for example an enzyme, a fluorochrome).
• a development system for example an enzyme, a fluorochrome
• Patent Application WO 2006/017549 A2 describes a method for the analysis of the phosphorylation of the proteins by flow cytometry. After fixing and permeabilization, the cells are incubated with phosphospecific antibodies coupled with fluorochromes. Following washing to remove the excess of non-fixed antibodies, the cells are analyzed with a flow cytometer.
• the ELISA Enzyme-Linked Immunosorbent Assay
• This heterogeneous assay technique is based on the capture of the protein of interest by a first antibody, this antibody being immobilized on a solid phase. The protein is then recognized by a second antibody specific to the post-translational modification. This second antibody is coupled with an enzyme (peroxidase, alkaline phosphatase, ⁇ galactosidase, acetylcholine esterase) capable of producing a chromogenic or photochemical reaction, or to a fluorophore
• an enzyme peroxidase, alkaline phosphatase, ⁇ galactosidase, acetylcholine esterase
• the ELISA technique makes it possible to quantify the modified protein.
• TGR BioSciences markets an assay kit under the name "SureFire" making it possible to measure the phosphorylation of the proteins Erk1 and Erk2.
• the modified and non-modified protein substrates are detected by means of their previous coupling with the fluorescent compound.
• Fluorescent Protein Following the phosphorylation of the PKC, the phosphospecific antibodies bind to the PKC 1 causing the fluorescent compound and the GFP to move closer together.
• FRET Fluorescence Resonance Energy Transfer
• US Patent 6,900,304 describes the use of chimeric proteins making it possible to measure the degree of phosphorylation of a substrate.
• the chimeric protein is constituted by a donor compound, a phosphorylable domain, a domain recognizing the phosphorylated amino acids and an acceptor compound. Following a phosphorylation, the spatial resolution of the phosphorylable domain and the domain recognizing the phosphorylated amino acids leads to a bringing together of donor compound and acceptor compound.
• Hideyoshi H et al. (FEBS Lett. 1997, 414: 55-60) describe the use of peptides coupled with ⁇ -acryloyl ⁇ -dimethlaminonaphthalene (Acrylodan) or N-(7- dimethylamino-4-methylcoumarinyl) maleimide (DACM) which are permeable at the cell membrane.
• Acrylodan ⁇ -acryloyl ⁇ -dimethlaminonaphthalene
• DAM N-(7- dimethylamino-4-methylcoumarinyl) maleimide
• the phosphorylation of the peptides is followed by measuring the reduction in the fluorescence emitted at 524 nm (acrylodan) or at 475 nm (DACM) after excitation of the fluorophores.
• Post-translational modification this term designates a chemical modification of a protein taking place after its translation, comprising the group transfer reactions on, or starting from, the protein or also of proteolysis.
• the following reactions are post-translational modification reactions: Mono ADP ribosylation; Poly ADP ribosylation; Acetylation; Glutathionylation; O-Glycosylation; N- Glycosylation; Methylation; Nitration; Phosphorylation; prenylation; Sumoylation; Ubiquitination; Proteolysis; Biotinylation; Glutamylation.
• Coupling domain/Coupling agent designate a pair of compounds capable of establishing between them a covalent or non-covalent bond with high affinity in the cell.
• the Coupling domain/Coupling agent pairs can be constituted by the following pairs: peptide sequence/antibodies specific to this peptide sequence, "Tag'Vanti-tag antibodies, suicide enzyme/suicide enzyme substrate, biotin/avidin.
• the Coupling domain/Coupling agent pairs are used in the invention for coupling a fluorescent compound with a protein substrate present in the cell, in other words for labelling a protein substrate with this fluorescent compound.
• “Measurement medium” this term designates the container in which the test is carried out.
• “Intact living cell” this expression designates living cells the membrane and intracellular integrity of which is preserved. Cells containing one or more vector(s) for heterologous expression are intact living cells within the meaning of the invention.
• Method in homogeneous medium method carried out in a liquid medium, in the absence of a solid phase.
• Permeabilization within the meaning of the invention, the permeabilization of cells comprises any treatment applied to a cell making it possible for compounds not permeable to the plasmic membrane to enter the cell.
• the lysis of cells is included in this definition.
• “Pair of FRET partners” designates a pair constituted by a fluorescent donor compound and a fluorescent acceptor compound capable, when they are in proximity to one another and when they are excited at the excitation wavelength of the fluorescent donor compound, of emitting a FRET signal. It is known that in order for two fluorescent compounds to be FRET partners, the emission spectrum of the fluorescent donor compound must partially cover the excitation spectrum of the fluorescent acceptor compound.
• “FRET signal” designates any measurable signal representative of a FRET between a fluorescent donor compound and a fluorescent acceptor compound. A FRET signal can therefore be a variation in the intensity or fluorescence lifetime of the fluorescent donor compound or the fluorescent acceptor compound.
• the method for the detection of post-translational modifications involves detecting by the FRET technique a protein or peptide substrate having undergone a post-translational modification in a functional living cell.
• the method according to the invention does not require the addition of any co-factor involved in the reaction (for example the addition of high concentrations of ATP for the kinase assays), nor of stabilizing products which are necessary in the formats of the prior art (for example Mg 2+ ions in the kinase activity assays).
• the method according to the invention which is precise and adaptable to screening at high flow rates, therefore makes it possible to study the post-translational modifications and test compounds for their ability to modulate these reactions under conditions very close to physiological conditions.
• the method according to the invention also makes it possible to study only one given enzyme.
• the invention relates to a method in homogeneous medium making it possible to detect a post-translational modification of a protein substrate, the post-translational modification taking place in the intact living cells.
• This method is based on the heterologous expression by the cell of a fusion protein comprising said protein substrate and a first coupling domain, via an expression vector previously introduced into the cell.
• the method according to the invention advantageously uses a pair of FRET partners in order to measure the protein substrate having undergone a post- translational modification: the labelling of the protein substrate having undergone the post-translational modification by the FRET partner fluorescent compounds is carried out on the one hand via a coupling domain/coupling agent pair as described below, and on the other hand by means of a binding domain specifically recognizing the site of the protein substrate having undergone the post-translational modification, according to the following diagram:
• Polypeptide protein substrate
• the two fluorescent FRET partner compounds will be situated in proximity to one another and generate a FRET signal.
• This method for detection in homogeneous medium of a post-translational modification of a protein substrate catalyzed by a cell enzyme is therefore characterized in that the post-translational modification reaction takes place in intact living cells, in that these cells comprise a heterologous expression vector coding for a fusion protein comprising the protein substrate and a first coupling domain and in that it comprises the following stages:
• a stage of permeabilization or lysis of the cells is implemented before Stage (ii) and/or (iii).
• the intensity of the signal measured when the preceding method is implemented of course depends on the quantity of protein substrate having undergone the post-translational modification, but also on the total quantity of protein substrate present in the measurement medium. Generally, the signal measured is all the more significant when there is protein substrate in the medium.
• the signals specific to a post-translational modification obtained in different measurement media are to be compared, it becomes necessary to standardize these signals since, for example, different populations of cells can exhibit different levels of expression of the heterologous DNA coding for the protein substrate.
• the method according to the invention when used in order to determine the effect of a potential modulating agent of a post- translational modification (for example, in a medicament screening approach), the fact of measuring the total protein substrate makes it possible to verify that the product to be tested does not result in the death of the cell.
• a particular implementation of the invention therefore involves measuring, in addition to the protein substrate having undergone the post-translational modification, a signal representative of the total quantity of protein substrate.
• This second signal can be used to standardize that corresponding to the protein substrate having undergone the post-translational modification, for example by calculating the following ratio: signal corresponding to the modified protein substrate/signal corresponding to the total protein substrate .
• This implementation is based on the one hand on the use of two pairs of FRET partners, one making it possible to measure the signal corresponding to the modified protein substrate and the other making it possible to measure the signal corresponding to the total protein substrate, and on the other hand on the expression by the cell of a fusion protein comprising the protein substrate as well as two coupling domains.
• a population of cells is distributed in two separate measurement media, for example in different wells of a multiwell plate, so as to be able to measure on the one hand the signal corresponding to the protein substrate having undergone the post-translational modification, and on the other hand the signal corresponding to the total quantity of protein substrate.
• This implementation of the method for the detection in homogeneous medium of a post-translational modification of a protein substrate catalyzed by a cell enzyme is characterized in that the post-translational modification reaction takes place in intact living cells, in that these cells comprise a heterologous expression vector coding for a fusion protein comprising (1) the protein substrate, (2) a first coupling domain and (3) a second coupling domain, different from the first coupling domain, said second coupling domain not being affected by the post-translational modification, and in that it comprises the following stages:
• a stage of permeabilization of the cells or of lysis of the cells is implemented before Stage (ii) or before Stage (iii) and/or (vi).
• the measurements carried out in one or other measurement medium can be carried out in any order: they can be carried out in parallel on an automated system, or one after the other.
• the two pairs of FRET partners may or may not have the same spectroscopic characteristics.
• the second and third fluorescent compounds can be identical but each must be bonded to a different coupling agent.
• This assay format illustrated by the diagram below can be, for example, implemented with the following reagents:
• the quantity of protein substrate having undergone a post-translational modification is measured in a first well using the antibody specific to the modified protein substrate coupled with the fluorescent donor compound (D1) as well as with the anti-tag 2 antibody coupled with the fluorescent acceptor compound A compatible with the fluorescent donor compound D1 for the establishment of a FRET.
• the total quantity of protein substrate is measured using the anti-tag 1 antibody coupled with a fluorescent donor compound D, which may be D1, but which must be compatible with the fluorescent acceptor compound A for the establishment of a FRET, as well as with the anti-tag 2 antibody coupled with the fluorescent acceptor compound A.
• the tags can also be contiguous: Reading of Well 1
• the protein substrate having undergone a post- translational modification and detection of the total protein substrate in a single measurement medium FRET Killer
• the protein substrate having undergone the post-translational modification and the total protein substrate are measured in the same measurement medium: this implementation makes it possible to standardize the variations that could be encountered from one measurement medium to the other in a very effective manner.
• This implementation is based, on the one hand, on the use of two pairs of FRET partners - one making it possible to measure the signal corresponding to the modified protein substrate and the other making it possible to measure the signal corresponding to the total protein substrate - and, on the other hand, on the expression by the cell of a fusion protein comprising the protein substrate as well as two coupling domains, as in the preceding implementation.
• a FRET signal suppressing agent is used.
• a first pair of FRET partners is introduced into the measurement medium (a pair specific to the total protein substrate or modified protein substrate, it does not matter which), then the FRET signal suppressing agent is in turn added to the medium, so as to "switch off 1 the first signal.
• the second pair of FRET partners is then formed in the measurement medium and the second signal can be measured.
• the FRET signal suppressing agents are described below.
• This implementation of the method for the detection in homogeneous medium of a post-translational modification of a protein substrate catalyzed by a cell enzyme is characterized in that the post-translational modification reaction takes place in intact living cells, in that these cells comprise a heterologous expression vector coding for a fusion protein comprising (1) the protein substrate, (2) a first coupling domain and (3) a second coupling domain different from the first coupling domain, said second coupling domain not being affected by the post-translational modification, and in that it comprises the following stages: (i) Incubation of the cells in the presence or absence of a compound to be tested capable of modulating the activity of said enzyme,
• Stages (iii)-(iv) and (vi)-(vii) can be reversed in order to measure firstly the signal corresponding to the total protein substrate then the signal corresponding to the modified protein substrate, from the moment when the FRET signal suppressing agent specifically suppresses the first signal emitted in the measurement medium.
• This format can be implemented, for example, with the following reagents:
• the quantity of protein substrate having undergone a post-translational modification is measured using the antibodies recognizing the modified protein substrate coupled with the fluorescent donor compound D1 and the anti-tag 2 antibody coupled with the fluorescent acceptor compound A.
• the FRET suppressing agent, specific to D1 and suppressing the FRET between D1 and A, and the anti-tag 1 antibody, coupled with the fluorescent donor compound D2 are added to the same well. This second reading is representative of the total quantity of protein substrate.
• the method according to the invention makes it possible to adapt the FRET technique to the measurement of post-translational modifications in a cell context.
• the FRET phenomenon has been widely described in the literature and is a concept known to a person skilled in the art. It is a quantum phenomenon which is produced between two fluorescent molecules close to one another (distance comprised between ten and one hundred Angstrom) and the emission spectrum of one of which (the fluorescent donor compound) partially covers the excitation spectrum of the other (the fluorescent acceptor compound). When the fluorescent donor compound is excited by a photon, it can transmit its energy to the fluorescent acceptor compound which is then in an excited state and emits light.
• a pair of FRET partners within the meaning of the invention is therefore constituted by a fluorescent donor compound the emission spectrum of which partially covers the excitation spectrum of the fluorescent acceptor compound.
• the concept of FRET partners is well known to a person skilled in the art who is capable, on the basis of the spectroscopic characteristics of the known fluorescent compounds, of selecting the pairs of fluorescent compounds compatible in terms of FRET. It may moreover refer to the work by Lakowicz (1999) Principles of fluorescence spectroscopy, 2 nd edition, Kluwer academic/plenum publishers, NY.
• FRET is used here in the broad sense and includes time-resolved FRET (TR-FRET).
• the FRET phenomenon can be detected by the measurement of different parameters of the fluorescence signal emitted either by the fluorescent donor compound, or by the fluorescent acceptor compound, or by both compounds.
• the most common techniques there can in particular be mentioned: - The measurement of the reduction in the donor's fluorescence induced by the FRET phenomenon,
• the expression "measurement of the FRET signal" used in the description of the invention designates any one of these techniques equally.
• the measurement of the fluorescence emitted by the fluorescent acceptor compound is nevertheless one of the preferred approaches for the implementation of the invention.
• the fluorescent compounds can be chosen from the following group: the luminescent proteins such as green fluorescent protein (GFP) or its variants, fluorescent proteins extracted from corals, phycobiliproteins, such as B- phycoerythrin, R-phycoerythrin, C-phycocyanin, the allophycocyanins, in particular those known by the name XL665; the luminescent organic molecules such as the rhodamines, the cyanines, the squaraines, the fluorophores known by the name BODIPY, the fluoresceins, the compounds known by the name Alexa Fluor; the supra-molecular complexes such as the rare earth cryptates, the rare earth chelates (in particular europium, terbium, samarium, dysprosium, neodymium chelates and cryptates); luminescent inorganic particles such as nanocrystals ("quantum dots").
• GFP green fluorescent protein
• phycobiliproteins
• the rare earth complexes are known compounds which are described for example in the patents US 4 761 481, US 5 032 677, US 5 055 578, US 5 106 957, US 5 116 989, US 4 761 481, US 4 801 722, US 4 794 191, US 4 637 988, US 4 670 572, US 4 837 169, US 4 859 777.
• Other chelates are compounds of a nonadentate ligand such as terpyridine (EP 403 593, US 5 324 825, US 5 202 423, US 5 316 909).
• the rare earth can be europium or terbium.
• the rare earth cryptates are described in particular in the patents EP 0 180492, EP 0601 113 and the application WO 01/96 877.
• the rare earth complex is a europium chelate or cryptate.
• the rare earth complex is preferably a rare earth cryptate with a pyridine unit, still more preferably with a trisbipyridine and pyridine-bipyridine unit.
• one of these partners must be conjugated, preferably covalently bonded, to an element recognizing said protein substrate having undergone the post-translational modification.
• one of the fluorescent compounds either the fluorescent donor compound or the fluorescent acceptor compound, is covalently bonded to a binding domain (antibody, aptamer etc.) capable of recognizing the site of the protein substrate having undergone the post- translational modification.
• the other member of the pair of FRET partners is covalently bonded to a coupling agent capable of binding, covalently or non- covalently, to a coupling domain present on the protein substrate (protein tag, suicide enzyme etc.).
• the binding domain capable of recognizing the site of the protein substrate having undergone the post-translational modification can be variable in nature: it can be, for example, an antibody, an antibody fragment or an aptamer binding specifically to the site of the protein substrate having undergone the post- translational modification.
• a useful antibody in the invention can be a complete antibody, or an antibody fragment which can be a Fab or F(ab)'2 or single-chain Fv fragment.
• the antibody can be recombinant or non- recombinant.
• the antigen used for the immunization will comprise a sequence of 5 to 100 amino acids, or 5 to 50 or 5 to 15 amino acids one of which is a phosphorylated serine, or threonine, or tyrosine.
• antibodies specific to post-translational modifications are commercially available. They are, for example, antibodies specific to phospho- serine, phospho-tyrosine, phospho-threonine (Upstate Biologicals, new England Biolabs etc.).
• the aptamers which are polynucleotide by nature are single-strand oligonucleotides which have been selected for their ability to bind specifically to a given molecule, in the case in point to a domain of a protein substrate having undergone a post-translational modification.
• the methods for the preparation and selection are known and in particular described in the patent US 5,567,588 (SELEX method).
• the aptamers which are peptidic by nature are constituted by a short sequence of 10 to 20 amino acids ("variable” domain conferring the specificity of the aptamer for a given target), the two ends of which are linked to a "scaffold", protein thus creating a structural constraint participating in the specificity of the peptidic aptamer.
• the methods for the selection and production of these aptamers are also known and described in the prior art.
• binding domains can recognize the sites of the modified protein substrate: in the case where the post-translational modification is a glycosylation, the binding domain can be a lectin such as WGA ("Wheat Germ Agglutinin").
• the phosphate groups present on the proteins having undergone a phosphorylation can be recognized by microbeads onto which metallic ions have been grafted.
• the binding domain specific to the modified substrate is therefore a microbead (technology known by the name of "IMAP” for "Immobilized Metal Ion Affinity").
• GST can be used as a specific binding domain recognizing the glutathion group grafted to the protein substrate.
• each of the members of the pair of FRET partners is conjugated, preferably covalently bonded, to a coupling agent (antibody, suicide enzyme substrate etc.) capable of binding, covalently or non-covalently, to a coupling domain present on the protein substrate (protein tag, suicide enzyme etc.).
• a coupling agent antibody, suicide enzyme substrate etc.
• the protein substrate comprises two different coupling domains, one for the fluorescent donor compound and one for the fluorescent acceptor compound.
• Fusion protein comprising the protein substrate and a coupling domain
• the cells on which the method according to the invention is carried out include an expression vector comprising a nucleic sequence coding for a fusion protein constituted by the protein substrate capable of undergoing the post-translational modification that is being studied, and at least one coupling domain which is recognized by the coupling agent bonded to one of the FRET partners.
• the choice of the protein substrate depends on the post-translational modification that is to be studied and a person skilled in the art can easily make this choice.
• Table 2 provides a few examples of protein substrates depending on the post-translational modifications studied.
• the protein substrate can have the same sequence as the "natural" substrate of the enzyme involved in the reaction that is to be studied: the expression vector can therefore contain a nucleic acid sequence coding for example for a protein receptor, a protein enzyme such as for example a kinase which can undergo a post-translational phosphorylation etc.
• the protein substrate can also be constituted by a fragment of the natural substrate, providing that this fragment comprises the domain recognized by the enzyme and the domain undergoing the post-translational modification.
• the protein substrate can be an artificial peptide substrate, such as for example the substrates described in the Application WO03/087400.
• the coupling domain fused with the protein substrate is a protein tag and the coupling agent is an antibody, an antibody fragment or also an aptamer specific to said tag.
• the tag can be any peptide sequence of 4 to 250 amino acids, preferably 4 to 50, and still more preferably 4 to 15 amino acids, providing that this tag does not impede the recognition of the substrate by the enzyme catalyzing the post-translational modification reaction.
• This tag can be naturally present in the protein substrate capable of undergoing the post- translational modification or be added as described in the experimental part.
• this protein tag is chosen from: glutathione S-transferase, avidin, a peptide constituted by 6 histidines, a peptide constituted by the amino acids 410-419 of the human Myc protein (EQKLISEEDL), a FLAG peptide with the sequence DYKDDDK, an influenza hemaglutinin epitope with the sequence YPYDVPDYA.
• the coupling domain fused to the protein substrate is a suicide enzyme and the coupling agent is a substrate of this enzyme.
• the suicide enzymes are proteins which have an enzymatic activity modified by specific mutations which confers upon them an ability to bind rapidly and covalently to a substrate. These enzymes are designated suicide enzymes as each one can bind only to one single fluorescent molecule, the activity of the enzyme being blocked by the fixing of the substrate.
• the mutant of an alkylguanine-DNA alkyltransferase (or "SnapTag” marketed by the company Covalys (WO 02/083937 A2).
• the coupling agent bonded to the fluorescent compound is benzyl-guanine or a benzylguanine derivative.
• the coupling domain is the enzyme Dihydrofolate reductase and the coupling agent is a Dihydrofolate reductase inhibitor, such as the antibiotic Trimethoprim or 5-(3,4,5-trimethoxybenzyl)pyrimidine-2,4-diamine (technology marketed under the name of "LigandLink” by Active Motif).
• Dihydrofolate reductase inhibitor such as the antibiotic Trimethoprim or 5-(3,4,5-trimethoxybenzyl)pyrimidine-2,4-diamine (technology marketed under the name of "LigandLink” by Active Motif).
• the expression vector present in the cell coding for a fusion protein and comprising at least one coupling domain is produced according to the technique known to a person skilled in the art. More precisely, this expression vector can be a plasmid into which there have been inserted, using restriction enzymes and ligases, the nucleic acid sequences coding for the fusion protein which is to be expressed by the cell. These sequences are integrated into the plasmid downstream of a promoter and in the same reading frame. Numerous expression vectors are commercially available.
• this fusion protein by the cell can be stable or transitory, according to whether or not the expression vector is integrated into the cell DNA.
• the method according to the invention has the advantage of allowing the detection of a post-translational modification taking place in a living cell, under conditions very close to physiological conditions. Nevertheless, once the post- translational modification reaction has taken place, it may be necessary to permeabilize the cell membrane prior to the addition of the FRET partner compounds in order to allow them to reach their target in the cell.
• the permeabilization of the cell membrane can be carried out by any appropriate method (Goncalves et al. (2000) Neurochem. Res. 25: 885-8).
• These methods include the addition of a detergent (for example: CHAPS, cholic acid, deoxycholic acid, digitonin, n-dodecyl-, 8-D-maltoside, lauryl sulphate, glycodeoxycholic acid, n-lauroylsarcosine, saponin or triton X-100) or of an organic alcohol (such as methanol or ethanol) to the culture medium.
• a detergent for example: CHAPS, cholic acid, deoxycholic acid, digitonin, n-dodecyl-, 8-D-maltoside, lauryl sulphate, glycodeoxycholic acid, n-lauroylsarcosine, saponin or triton X-100
• an organic alcohol such as methanol or ethanol
• a person skilled in the art is able to choose the permeabilizing agent and adapt the experimental conditions (in particular its concentration and duration of incubation) in order to permeabilize the cells satisfactorily, i.e. in such a manner that the pairs of FRET partners can penetrate into the cell.
• permeabilization includes the lysis of the cells: once the post-translational modification has taken place in a cell context, it is no longer necessary to maintain the integrity of these cells.
• the addition of the FRET partners allowing the detection of the protein substrate having undergone the modification and/or optionally those allowing the detection of the total protein substrate, can be carried out on a cell lysate and not necessarily on a population of intact living cells.
• fluorescent conjugates which are capable of passing through the plasmic membrane, either because they are "naturally” capable of this because of their chemical structure, or because they comprise a domain allowing them to pass through the cell membrane.
• esters which mask the charged groups during the passage through the lipid bilayer come within the category of the compounds named "pro-drugs " and refer to compounds which are rapidly transformed in vivo in order to produce the "parent" compound following hydrolysis under physiological conditions (T. Higuchi and V. Stella (1975) in "Pro-drugs as Novel Delivery Systems", Vol. 14 of the A.C.S. Symposium Series, American Chemical Society). Examples include mainly the pivaloyl-oxymethyl, acetoxymethyl groups as well as the glycol esters (Nielsen and Bundgaard (1984) Int. J. of Pharmacy 39: 75-85). When this technique is used, one of these esters is grafted covalently onto the fluorescent compound.
• viral peptides grafted covalently onto the fluorescent compound.
• Certain viral peptides make it possible to convey the fluorescent compound through the cell membrane.
• viral peptides there can be mentioned the analogues of "penetratin” and "transportan” (Langel et al. (2000) Bioconj. Chem. 11: 619-626), the poly-Arginines (Wender et al. (2003) Org. Lett. 5(19): 3459-3462), the peptoids (analogues of peptides carrying guanidine groups (Wender et al. (2000) Proc. Natl. Acad. Sci.
• At least one fluorescent compound comprises a domain allowing it to pass through the plasmic membrane, this unit being selected from the following groups: esters such as pivaloyl-oxymethyl ester, acetoxymethyl ester, or glycol esters; viral peptides carried by membrane transporters such as penetratin and its analogues, transportan and its analogues, the polyarginine groups, the peptoids carrying guanidine groups, such as the oligoguanidinium groups; cholesterol groups, vitamin E or aliphatic chains such as undecyl or 1 ,2-di-O-hexadecyl-glycerol chains.
• esters such as pivaloyl-oxymethyl ester, acetoxymethyl ester, or glycol esters
• viral peptides carried by membrane transporters such as penetratin and its analogues, transportan and its analogues, the polyarginine groups, the peptoids carrying guanidine groups, such as the oligoguani
• a particularly advantageous implementation of the invention involves measuring the signal corresponding to the protein substrate having undergone a post- translational modification and the signal corresponding to the total protein substrate in the same measurement medium.
• a FRET suppressing agent is used as described above.
• FRET signal suppressing agent a compound which causes a FRET signal reduction of at least 70% relative to the signal measured in the absence of this compound.
• the FRET signal suppressing agents used in the method according to the invention do not disturb the biological event studied (post-translational modification) to the extent that they act at the level of one of the fluorescent compounds involved in the FRET, and not at the level of the biological event studied. They have no effect on the distance separating the molecules involved in the biological event.
• a compound In order to determine whether a compound is a FRET signal suppressor within the meaning of the invention, it can be placed in contact with a pair of FRET partner fluorescent conjugates emitting a FRET signal, for example two fluorescent conjugates recognizing the same molecule, or also two fluorescent conjugates one of which comprises a biotin and the other streptavidin.
• the FRET signal emitted by the reaction medium is measured in the presence and in the absence of said compound, the FRET signal suppressors being those which lead to a reduction in signal of at least 70%. This simple test allows a person skilled in the art to isolate FRET suppressing agents within the meaning of the invention.
• FRET suppressing agents can be different in nature and have different functions, but they make it possible, in all cases, to suppress the FRET signal emitted by a given donor-acceptor pair.
• the FRET suppressing agents can be of four types.
• These agents have a domain allowing specific and non-covalent binding with the fluorescent compound. They can be chosen from: proteins, in particular antibodies or fragments of antibodies, peptides or aptamers, each having a binding domain for one of the FRET partner fluorescent compounds.
• FRET signal suppressing agents are, in the case of a FRET involving a rare earth chelate or cryptate, the compounds capable of binding non-covalently to rare earth cryptates or chelates, such as for example: proteins, in particular antibodies or fragments of antibodies, peptides, or aptamers possessing a binding domain for a rare earth cryptate or chelate.
• Still more preferred FRET signal suppressing agents are the anti-rare earth chelate or anti-rare earth cryptate antibodies.
• the anti-cryptate antibodies are produced by the technique well known to a person skilled in the art, by immunizing a mammal with an antigen.
• the antigen In the case where the antigen is small in size, as is the case with rare earth cryptate, it must be coupled with an immunogen-carrying molecule.
• the cryptate is functionalized, as described in the patent EP 321 353.
• an alkylamine arm is grafted onto the cryptate.
• the carrier molecules can be chosen from: bovine serum albumin (BSA) or cationic BSA (cBSA), KLH (Keyhole Limpet Hemocyanine), thyroglobulin, ovalbumin.
• BSA bovine serum albumin
• cBSA cationic BSA
• KLH Keyhole Limpet Hemocyanine
• thyroglobulin ovalbumin.
• the carrier molecules can also be liposomes or synthetic carrier molecules such as L-lysine polymers, or L-glutamic acid, ficoll, dextran, or also polyethylene glycol.
• These carrier molecules generally comprise functional groups which react with the functionalized cryptate, or such groups can be introduced by standard techniques.
• a rare earth cryptate carrying an alkylamine group is conjugated with the BSA.
• the immunogen thus obtained is then mixed with an adjuvant, such as for example Freund's adjuvant, in order to form a solution.
• an adjuvant such as for example Freund's adjuvant
• Mammals - for example mice - are immunized by sub-cutaneous injection of this solution, and after a period necessary for the induction of immunity, the sera of the animals are collected and the polyclonal antibodies purified, for example by affinity chromatography.
• the anti-cryptate monoclonal antibodies are produced using various techniques known to a person skilled in the art.
• the techniques originating from the works of Kohler and Milstein a few weeks after the immunization, the spleen of the mouse immunized with the antigen is removed.
• a mixture of lymphocytes and plasmocytes originating from this spleen is fused in vitro with myelomatous cells in the presence of a cell fusion inducer, such as polyethylene glycol.
• a mutant myelomatous cell line, devoid of hypoxanthine guanosine phosphoribosyl transferase (HGPRT) is used in order to make it possible to easily select the hybrid cells.
• HGPRT hypoxanthine guanosine phosphoribosyl transferase
• the cells are cultured in a medium containing hypoxanthine, aminopterine (methotrexate) and thymine (HAT medium) in order to eliminate the non-fused myelomatous cells and to select the hybridomas of interest.
• the non-fused spleen cells die as they are not capable of proliferating in vitro.
• the hybrid cells survive.
• the hybridomas thus obtained are cultured in the well of a cell culture plate. The supernatants of these wells are tested for the presence of specific anti- rare earth cryptate antibodies in a simple screening test such as ELISA or
• the hybridomas are then cloned and can be injected into mammals in order to induce myelomes secreting a large quantity of anti-cryptate antibodies in the ascitic liquid.
• the polyclonal or monoclonal anti-rare earth cryptate antibodies obtained can then be tested for their ability to suppress the FRET signal emitted by a pair of FRET partners comprising said rare earth cryptate as fluorescent energy donor compound.
• the procedure as described above and in Example 1 presented below can be followed.
• FRET suppressing agents acting by decoupling of the fluorescent compound with the biological event As described above, the study of biological events using the FRET phenomenon is based on the labelling of molecules involved in the biological event by FRET partner fluorescent compounds. If this labelling is carried out in non-covalent manner, via binding partners, it is possible to uncouple one of the fluorescent compounds from the biological event.
• a molecule involved in the biological event is covalently bonded to a member of a pair of binding partners (for example a single- strand oligonucleotide), and that fluorescent compound is covalently bonded to the other member of this pair (for example a complementary single-strand oligonucleotide), then the addition to the measurement medium of the first member of this couple (the first single-strand oligonucleotide, in free form) will uncouple the labelling of the biological molecule by the fluorescent compound, by a competition phenomenon according to the following diagram:
• FRET signal suppressing agents are therefore members of pairs of binding partners, and can of course only be used as FRET signal suppressing agents if their partner is grafted onto the molecule involved in the biological event studied.
• DNP/ anti-DNP antibodies in which DNP represents dinitrophenol
• GST/ anti-GST antibodies in which GST represents glutatione S-transferase
• biotin/avidin 6HIS/ anti-6HIS antibodies in which 6HIS is a peptide constituted by 6 histidines
• Myc/ anti- Myc antibodies in which Myc is a peptide constituted by the amino acids
• the FRET suppressing agents can reduce the stability of the fluorescent compound by entering into competition either with the rare earth for binding to the chelate, or with the chelate for binding to the rare earth.
• the addition to the measurement medium of an ion which will enter into competition with the rare earth for binding to the chelate can encourage the formation of a new non-fluorescent chelate/ion complex .
• Such an ion can be the Manganese Mn 2+ ion in the case of the rare earth chelates.
• fluorescent compounds are sensitive to the variations in ionic strength of the medium: this is the case in particular with the fluorescent protein compounds comprising several sub-units linked by electrostatic bonds, and the quaternary structure of which is destabilized during a reduction in the ionic strength of the medium.
• allophycocyanin which dissociates under these conditions.
• FRET suppressing agents results in a fluorescence extinction effect (also called “quenching").
• uric acid which, in the case where the fluorescent compound is a rare earth chelate or cryptate, can cause oxidation-reduction reactions of the rare earth which can lead to a suppression of the FRET.
• fluorescent compounds are sensitive to variations in pH and the agents modifying the pH can in this case also be used as FRET signal suppressing agents.
• the agents modifying a fluorescent compound emission or absorption spectrum can be used in the methods according to the invention, providing that they effectively cause a suppression of the FRET signal within the meaning of the invention. This characteristic can be tested simply as mentioned above. Vl. Enzyme catalyzing the post-translational modification and other proteins involved in the post-translational modification
• the enzyme catalyzing the post- translational modification is expressed by an expression vector integrated by the cell in a stable or transitory manner.
• the sequences of these enzymes are available in the literature and their expression comes within the routine techniques for a person skilled in the art.
• This implementation makes it possible to overexpress the enzyme involved and therefore to amplify the signal measured since a larger quantity of protein substrate is potentially modified.
• the overexpression of the enzyme increases the specificity of the signal with respect to the other cell enzymes and therefore allows the study of a given enzyme.
• This implementation also makes it possible to control the expression of the enzyme if the expression vector comprises a regulation domain such as an inducible promoter or an "enhancer" sequence.
• Certain enzymes catalyzing a post-translational modification are not constitutively active and must be activated.
• the methods according to the invention can therefore comprise an additional stage of activation of the enzyme involved in the reaction studied.
• This stimulation can be: an osmotic shock, thermal shock, oxidative stress induced by a chemical compound (for example by the addition of H2O2 or diamine to the culture medium).
• a chemical compound for example by the addition of H2O2 or diamine to the culture medium.
• Carcinogenic compounds, heavy metals (for example mercury, cadmium etc.) or pollutants can also be used as chemical activators.
• This stimulation can also be biochemical in nature by the addition, to the culture medium, of growth factors (such as the EGFs, the FGFs, the CSFs 1 the HGFs, IGFs, ILGFs, NGFs, PDGFs, VEGFs), cytokines (such as the interleukins IL-1, IL-2, IL-6, IL-8), the interferons IFN- ⁇ and IFN- ⁇ , TNF ⁇ , TNF ⁇ , growth hormones (such as PL, GH, PrI) or neuromediators (such as acetylcholine, glycine, glutamate, GABA, dopamine, noradrenaline, histamine).
• growth factors such as the EGFs, the FGFs, the CSFs 1 the HGFs, IGFs, ILGFs, NGFs, PDGFs, VEGFs
• cytokines such as the interleukins IL-1, IL-2, IL-6, IL-8
• the method according to the invention is implemented using cells expressing a protein involved in the activation cascade leading to the post-translational modification.
• proteins can, for example, be a transmembrane receptor, such as a receptor coupled to G protein, or an enzyme producing an intracellular messenger (such as adenylate cyclase) the activation of which results, via an intracellular signalling cascade, in the modification of the protein substrate capable of undergoing the post- translational modification.
• the cells contain an expression vector integrated into the cell in a stable or transitory manner, and coding for a protein involved in the activation route leading to the post-translational modification.
• the invention also relates to cells suited to the implementation of the methods according to the invention.
• These cells suited to the study of a post-translational modification are characterized in that they comprise: a) an expression vector coding for a fusion protein comprising the protein substrate and one or two coupling domains; and b) an expression vector comprising the nucleic acid sequence coding for the enzyme catalyzing said post-translational modification or for a protein involved in the activation cascade leading to the post-translational modification.
• the protein involved in the activation cascade leading to the post-translational modification is, preferably, a membrane receptor or an enzyme producing an intracellular massager.
• these expression vectors can for example be plasmids.
• the cells can in particular be cells of mammals, in particular human cells.
• the expression vectors are integrated into the cellular DNA.
• the expression vectors are integrated into the cellular DNA and the cells are immortalized cells, which makes it possible to obtain stable cell lines, which are particularly advantageous for studying a post-translational modification under easily reproducible conditions.
• the co-transfection of expression vectors into a cell and the obtaining of immortal cell lines expressing "exogenous" proteins in a stable manner are techniques known to a person skilled in the art.
• the method according to the invention could not be limited to a given post- translational modification.
• the work carried out by the Applicant can be easily transposed to the majority of post-translational modifications involving a group transfer onto a protein substrate, a group cleavage present on a protein substrate, or also a protein substrate cleavage.
• the method according to the invention is particularly suited to the study of the following post-translational modifications: mono ADP ribosylation: transfer of an ADP-ribose to an Arginine or Cysteine residue of the protein to be modified, a reaction catalyzed by a mono ADP-ribosyl transferase.
• the mono ADP ribosylation plays a fundamental role in the cell signalling, as well as in the modification of the cytoskeleton by targeting the actin as well as the desmin filaments.
• poly ADP ribosylation transfer of polyADP-ribose to a glutamic acid residue of the protein to be modified, a reaction catalyzed by a poly ADP-ribose polymerase.
• PARP Poly ADP ribosylation of nuclear proteins by the Poly ADP ribose polymerases
• Phosphorylation transfer, by a Kinase, of the ⁇ phosphate of ATP to a hydroxyl group of a Serine, Threonine, Tyrosine or Histidine of the protein to be modified.
• the phosphorylation of proteins is a central element in the transduction of the signal within the cell.
• the kinase proteins represent a large family of enzymes sharing a common structure. These enzymes control a large number of intracellular mechanisms which include the transcription and translation of genes, the regulation of the cell cycle, the growth and differentiation of cells, the cell metabolism as well as apoptosis. The deregulation of the kinasic activities is frequently involved in cell dysfunctions.
• the main protein kinase families are listed in Table 1.
• Acetylation transfer of an acetyl group, by acetyltransferases, from the acetyl-CoA to the ⁇ -NH2 functions of the lysine residues of the protein to be modified.
• Acetylation is a post-translational modification which mainly targets the histones. The degree of acetylation of the histones is strongly correlated with the transcriptional activity of the cell. Contributing to the increase in the transcriptional activity, numerous transcription factors are also acetylated.
• the tumor suppression protein p53 is also acetylated by p300/CBP.
• Glutathionylation transfer of a glutathione group to a Cysteine residue of the protein to be modified as a result of cell stress.
• This reaction is not catalyzed by a particular enzyme. It is therefore regulated in the cell by the intracellular concentration of the reagents involved.
• - N-Glycosylation the oligosaccharyl transferases transfer, from the dolichol pyrophosphate, an oligosaccharide of 14 sugars Glc 3 Man 9 GlcNAc 2 (GIc: Glucose, Man: Mannose, GIcNAc: N acetyl glucosamine) to an asparagine residue (Asn) included in the sequence Asn-X-Ser or Asn-X-Thr (X being able to be any amino acid with the exception of proline) of the protein to be modified.
• the N-glycosylation takes place in the endoplasmic reticulum and the Golgi apparatus and targets the proteins intended to be secreted or expressed at the cell surface.
• O-Glycosylation transfer of the GIcNAc group from UDP-GIcNAc (Uridine di-phosphate-N-acetyl glucosamine) to the Serine and Threonine residues of the protein to be modified.
• UDP-GIcNAc Uridine di-phosphate-N-acetyl glucosamine
• the O-glycosylations target numerous nuclear and mitochondrial cytoplasmic proteins.
• Methylation transfer of a methyl group from the S-adenosyl-methionine to an arginine residue of the protein to be modified.
• Eight protein arginine methyl transferases PRMT 1-8) exist in a mammal capable of this reaction.
• the methylated proteins often contain repetitions of the RGG or GRG unit.
• the methylation of the proteins plays multiple roles in the cell mechanisms.
• Proteolysis the peptidases are capable of splitting the proteins using a water molecule to cut the peptide bond.
• the endopeptidases recognize a primary sequence, a secondary or tertiary structure within the substrate and cut the protein after a determined amino acid.
• the exopeptidases digest a polypeptide chain from the N or C terminal end.
• the proteolysis phenomena modulate the activity, the role, the location and the fate of numerous proteins. Proteolysis can lead to the generation of active biomolecules starting from the zymogen, to the destruction of a bioactive protein, or constitute a prerequisite for other post-translational modifications.
• Prenylation covalent addition of a lipid group of farnesyl (15 carbons) or geranylgeranyl type (20 carbons) by creation of a disulphide bridge with a cysteine situated close to the C-terminal end of the protein to be modified.
• Prenylation allows the membrane anchoring of the protein but also plays a role in the protein-protein interactions.
• Farnesyltransferase and geranylgeranyltransferase 1 recognize the same unit comprising a cysteine (CAiA 2 X box) and catalyze the transfer of a lipid group to this cysteine.
• X is a Serine, Methionine, Alanine or Glutamine
• the protein is prenylated by farnesyltransferase; if X is a Leucine then this enzyme is geranylgeranyltransferase 1.
• Geranylgeranyltransferase 2 transfers the geranylgeranyl group to cysteines situated at the C-terminal end of the protein, said cysteine being comprised in one of the following sequences: -XXXCC, -XXCXC, -XXCCX 1 -XCCXX or -CCXXX.
• Ubiquitination attachment of an ubiquitin (protein with 76 amino acids) in covalent manner by an isopeptide bond joining the ⁇ -amino group of a lysine residue of the target protein to the C-terminal glycine of the ubiquitin.
• This process requires the action of three enzymes: a ubiquitin activation enzyme (E1), a ubiquitin transport enzyme (E2) and a ubiquitin ligase (E3).
• E1 , E2 and E3 Very numerous forms of these enzymes E1 , E2 and E3 exist.
• a protein can be mono- ubiquitinated on different lysines, or the cycle can be repeated several times, the fixed ubiquitin being ubiquitinated in its turn, leading to an extension of the chain, called poly-ubiquitination (3 to 5 ubiquitins).
• poly-ubiquitination 3 to 5 ubiquitins.
• either the protein is directed to the proteasome S26 where it is degraded, or it affects the tolerance to DNA lesions, the inflammatory response, the circulation and protein synthesis. For its part monoubiquitination plays a role in the circulation of the proteins.
• Nitration covalent bond between an NO 2 and a tyrosine or cysteine of the protein to be modified. This post-translational modification is not catalyzed by an enzyme and therefore depends on the concentration of the reagents involved in the cell. The nitration of the proteins modifies their function and their degradation.
• the method of study of post-translational modifications according to the invention is implemented on cells expressing a protein substrate capable of undergoing the post-translational modification studied, this protein substrate comprising at least one coupling domain allowing its detection by a FRET technique.
• Table 2 illustrates a certain number of post-translational modifications which can be studied using the method according to the invention: in the case of the modifications involving a group transfer catalyzed by an enzyme expressed by the cell (column 2) from a donor group (column 3) to an amino acid (column 4) present on the protein substrate expressed in a stable or transitory manner by the cell (column 5), one of the fluorescent compound members of a pair of FRET partners is covalently bonded to a binding domain specific to the post- translational modification (column 6).
• the method according to the invention is particularly useful for testing the ability of certain so-called “candidate” compounds to modulate post-translational modifications.
• the detection method according to the invention is implemented in the presence and in the absence of such compounds and the signals obtained are compared. These signals can also be compared with the signals obtained by incubating the cells with known modulators - inhibitors or activators.
• the method according to the invention makes it possible to exclude the "non- physiological" false positives obtained during the implementation of the in vitro technique of the prior art: these compounds are those which have an effect in vitro but are, in fact, incapable of reaching their target under physiological conditions.
• Another aspect of the invention relates to a cell suited to the study of a post- translational modification as described previously characterized in that it comprises: a) an expression vector coding for a fusion protein comprising the protein substrate and one or two coupling domains; and b) an expression vector comprising the nucleic acid sequence coding for the enzyme catalyzing said post-translational modification and/or the nucleic acid sequence coding for a protein involved in the activation cascade leading to the post-translational modification, such as a membrane receptor or an enzyme catalyzing the production of an intracellular messenger.
• the cell according to the invention is characterized in that said expression vectors are integrated into the cellular DNA.
• the cell according to the invention is, preferably, an immortalized cell.
• the cell according to the invention can be of any kind. It is preferably a mammal cell, in particular a human cell.
• Figure 4 Comparison of the measurement of the phosphorylated protein substrate by the two approaches (reading in separate wells or reading in a single well)
• Figure 5 Comparison of the measurement of the total protein substrate by the two approaches (reading in separate wells or reading in a single well)
• Figure 7 Inhibition of the activity of the kinase by staurosporine.
• Figure 8 Co-transfection of Akt kinase and substrate - Measurement of total expressed substrate
• Detection of the expressed substrate by using either anti c-myc- europium cryptate as donor compound, and anti-Flag-XL665 as FRET acceptor compound, or anti c- myc- europium cryptate and a suicide enzyme Snaptag and increasing concentrations of its substrate Benzyl Guanine (BG) conjugated to the fluorescent acceptor compound Dy647.
• BG Benzyl Guanine
• Detection of the phosphorylated substrate by using either the antibody STK- europium cryptate as donor compound and anti-Flag-XL665 as FRET acceptor compound, or the antibody STK- europium cryptate as donor compound and a suicide enzyme Snaptag and increasing concentrations of its substrate Benzyl Guanine (BG) conjugated to the fluorescent acceptor compound Dy647.
• BG Benzyl Guanine
• Example 1 Measurement of the phosphorylation of an Akt protein substrate by this enzyme, transfection of the protein substrate alone or co-transfection of the protein substrate and the enzyme.
• This example illustrates the use of the method described in the invention for measuring the phosphorylation of a protein substrate by a homogeneous TR- FRET technique.
• This example also underlines the importance of the co- transfection of the cells with, on the one hand, a plasmid coding for an enzyme inducing a post-translational modification, and on the other hand a target peptide sequence.
• the following sequence represents the sense strand (5'-3') coding for a fusion protein comprising: the c-myc tag (underlined), a generic substrate recognized by the serine/threonine kinases (in bold) and the FLAG tag (dotted underlining), flanked in position 5' by part of the restriction site of BamH1 and in position 3' by part of the restriction site of Xho1: GATCCGAACAAAAACTCATCTCAGAAGAGGATCTGAAGAAGCTCAATCGTAC
• the double-strand oligonucleotide is obtained by hybridizing the following two oligomers: - Sense:
• the sequence is inserted into the pSEMS plasmid (from Covalys) by mixing 1 ⁇ l of
• 8000 HEK293 cells are either transfected with increasing quantities of plasmid coding for the substrate alone, or co-transfected with the same quantities of plasmid coding for the substrate and 25 ng of Akt1-pcDNA 3.1 (Invitrogen Corp. Cat N° V790-20)
• the co-transfection is carried out in the presence of Lipofectamine 2000 (Invitrogen corp. Cat N° 11668-019) and OPTI-MEM medium (Gibco Cat N° 31985).
• the cells are then cultured for 48 hours at 37°C in 25 ⁇ l of DMEM medium (Gibco Cat N° 11965-092), to which 10% FCS (Hyclone Cat N°SV30014-03) and 1% antibiotic and antifungal (Gibco Cat N° 15240-062) are added in 384-well plates (Proxiplate 384, Perkin-Elmer Cat N° 6006280).
• the cells are lysed in 50 mM Hepes buffer, pH7, containing 0.1% BSA 1 20 mM EDTA, 0.8 M potassium fluoride and 2% triton X100.
• This same buffer contains 1.8 ng of phosphospecific antibodies (STK antibody, Upstate Cat N° 35-002) conjugated with the donor (europium cryptate) and 40 ng of anti-FLAG conjugated with the acceptor (cross-linked allophycocyanin, XL 665, CIS bio international Cat N° 61FG2XLA).
• STK antibody Upstate Cat N° 35-002 conjugated with the donor (europium cryptate)
• 40 ng of anti-FLAG conjugated with the acceptor cross-linked allophycocyanin, XL 665, CIS bio international Cat N° 61FG2XLA.
• the FRET signals are measured on an Acquest 384 fluorimeter (Molecular Device) in TR-FRET mode at 620 nm (emission wavelength of rare earth cryptate) and 665 nm (emission wavelength of allophycocyanin) after excitation by a flash lamp with a bandwidth comprised between 330 and 380 nm.
• the ratio between the fluorescence emitted at 665 nm (fluorescence of the acceptor) and the fluorescence emitted at 620 nm (fluorescence of the donor) (Ratio 665/620) is representative of the FRET occurring between the donor (europium cryptate) and the acceptor (Allophycocyanin). This FRET is proportional to the spatial proximity between the donor and the acceptor.
• the delta F (%) (DF) corresponds to: (Ratio 665/620 of the sample x 10000)- (Ratio 665/620 of the negative control x 10000) X100
• the negative control signal corresponds to the signal obtained with the non- transfected cells.
• the cells are transfected with the plasmid coding for the substrate alone or co- transfected with this same plasmid coding for the substrate and a plasmid coding for Akt1.
• the phosphorylation of the substrate is detected using a phosphospecific antibody coupled with europium cryptate (donor) (Ref. CIS biointernational, standard tris bipy extinguished by the FRET killer), and an anti-FLAG antibody coupled with allophycocyanin (Ref. XL665 CIS bio international).
• the FRET measured is proportional to the spatial proximity between the donor and the acceptor. This proximity results from the fixing of the phosphospecific antibodies to the phosphorylated protein substrate on the one hand and the fixing of the anti-FLAG to the FLAG sequence on the other hand.
• Figure 1 confirms that the FRET measured is proportional to the quantity of phosphorylated protein substrate and therefore that the method according to the invention makes it possible to detect the phosphorylation of a protein substrate by the kinase Akt1, this phosphorylation having taken place in the intracellular membrane.
• the same protein substrate can in general be phosphorylated by several kinases.
• the co-transfection of the kinase and its substrate makes it possible to detect the contribution of this particular kinase to the phosphorylation of the protein substrate, and thus to study the effect of (potentially inhibiting) compounds on this kinase.
• Figure 1 shows that when the cell is transfected by the only plasmid coding for the protein substrate, the protein substrate is phosphorylated by the endogenous kinases, including Akt1.
• the co-transfection with the plasmid coding for the protein substrate and the plasmid coding for the kinase Akt1 makes it possible to increase the quantity of protein substrate phosphorylated specifically by Akt1.
• Example 2 Measurement of the phosphorylation of a generic protein substrate by Cam kinase II, a non-constitutively active kinase, in the presence and in the absence of ionomycin.
• a kinase is not permanently active, even if the molecules of a population of kinase can be at different levels of activation. This is the case with the Cam kinase Il studied in this example, which is here activated by the addition of ionomycin to the medium.
• This example shows that the method according to the invention can be used with success to detect an intracellular modification (here, phosphorylation of a protein substrate by the Cam kinase II) resulting from an extracellular stimulation (here, chemical stimulation by ionomycin).
• 8000 cells HEK293 are either transfected with increasing quantities of plasmid coding for the substrate alone (Identical to Example 1), or co-transfected with the same quantities of plasmid coding for the substrate and 25 ng of CamKII ⁇ -pcDNA 3.1 (plasmid coding for Cam kinase II). The transfection is carried out as described in Example 1.
• the cells are then cultured for 48 hours at 37°C in DMEM medium, comprising 10% foetal calf serum and 1% antibiotic and antifungal, then for 16 hours in the same medium without serum.
• DMEM medium comprising 10% foetal calf serum and 1% antibiotic and antifungal
• the cells are stimulated for 5 min in the presence of ionomycin 1 ⁇ M (Sigma), and lysed as described above.
• the phosphorylation of the protein substrate is detected as described in Example 1.
• Figure 2 shows that in the absence of stimulation by ionomycin, the method according to the invention does not make it possible to detect phosphorylated protein substrate, whatever the quantity of plasmid coding for the protein substrate present in the cell.
• the signal measured is much greater than in its absence. Moreover, this signal is positively correlated with the quantity of plasmid coding for the transfected substrate in the cell.
• the ionomycin can be replaced with a compound to be tested and the signals obtained in the absence and in the presence of this compound can be compared.
• Certain inhibitor compounds in particular the allosteric inhibitors, become fixed to the inactive kinase and stabilize it in this state. These same compounds have little or no activity on the kinase when it is active.
• the method according to the invention makes it possible, by adding a compound to be tested (potential allosteric inhibitor) to the measurement medium before the addition of ionomycin, to detect such allosteric inhibitors.
• Example 3 Detection of the inhibition by staurosporine of the phosphorylation of a generic protein substrate by Akt1: parallel measurements of the phosphorylated protein substrate and the total protein substrate in 2 different wells
• Example 3 shows that the method of the invention makes it possible to test the ability of a compound to inhibit a kinase.
• the cells are co-transfected and cultured as described in Example 1. After culture for 48 hours, they are incubated for 1 hour in the presence of increasing concentrations of staurosporine, an known kinase Akt1 inhibitor. The cells are then lysed and the phosphorylated protein substrate detected as described in Example 1. In parallel, in a second well, cells are treated in identical manner. After lysis, the total quantity of protein substrate is measured using an anti-c-myc antibody coupled with europium cryptate (2.9 ng /well) (CIS bio international Cat N° 61 MYCKLA) and an anti-FLAG antibody coupled with allophycocyanin (40 ng/well). Results
• the peptide sequence target is inserted between two peptide sequence tags (c- myc and FLAG).
• the expressed quantity of these two sequences is therefore equivalent to the expressed quantity of protein substrate.
• the measurement of the FRET occurring between an c-myc antibody coupled with a donor and an anti- FLAG antibody coupled with an acceptor is therefore representative of the total quantity of protein substrate expressed by the cell.
• Figure 3 shows, in two separate wells, for each concentration of staurosporine, the measurement of the signal corresponding to the phosphorylated protein substrate on the one hand, and the measurement of the signal corresponding to the total protein substrate on the other hand. It is noted that the signal corresponding to the phosphorylated protein substrate reduces with increasing concentrations of Akt1 inhibitor, since the signal corresponding to the total protein substrate remains constant whatever the dose of inhibitor.
• the method according to the invention therefore makes it possible to assert that the reduction in the signal corresponding to the phosphorylated protein substrate is linked to the action of the inhibitor and not to a reduction in the quantity of protein substrate expressed in the cell.
• the method according to the invention makes it possible to detect an inhibitor of the post- translational modification studied (here phosphorylation by Akt1).
• Example 4 is an illustration of the method according to the invention which allows the detection of the protein substrate having undergone a post-translational modification and the detection of the total protein substrate in a single measurement medium (FRET killer).
• Figures 4 and 5 show the comparison of the measurement of the quantity of phosphorylated protein substrate and total protein substrate, under two measurement conditions: measurement carried out in two different wells, or measurement carried out sequentially, in the same well, using a FRET suppressing agent.
• the cells are co-transfected with, on the one hand, a plasmid coding for the protein substrate labelled by the c-myc and flag tags and, on the other hand, a plasmid coding for Akt1 , as described in Example 1.
• the cells are then treated as described previously with straurosporine.
• Measurement of the FRET signals corresponding to the phosphorylated protein substrate and to the total protein substrate is carried out either: - In two separate wells after the lysis stage,
• the lysate is first placed in the presence of a phosphospecific antibody, coupled with tris-bipyridine europium cryptate (CIS bio international, formula below), and an anti-FLAG antibody coupled with allophycocyanin (in the same quantities as those described in Example 1).
• the plate is incubated for 1 hour at ambient temperature before the measurement of the quantity of phosphorylated protein substrate by TR-FRET.
• FIGS. 4 and 5 show the results of the measurements of the phosphorylated and total protein substrate according to the two methods.
• Akt DN signifies that the cells have been transfected with a plasmid coding for a negative dominant mutant of Akt, i.e. which does not catalyze by phosphorylation but which is capable of binding to staurosporine.
• Figure 4 shows that, in both cases, a signal corresponding to the phosphorylated protein substrate is measured, and that this signal appears to be sensitive to staurosporine only in the case where it is added to the measurement medium at high concentrations (2 ⁇ M).
• Figure 5 shows that in both cases (measurements carried out in the same well or in two separate wells), a signal corresponding to the total protein substrate is measured. It is noted that the signals corresponding to the total protein substrate vary from one well to the other. In particular, the wells into which 20 nM of staurosporine have been introduced in fact contain far more protein substrate than the other well.
• Figure 6 shows the usefulness of standardizing, for each experimental condition, the signal corresponding to the phosphorylated protein substrate by the signal corresponding to the total protein substrate, in order to be rid of the inter-well variations which mask, for example, the effect of 20 nM staurosporine in Figure 4.
• Figure 6 thus demonstrates the inhibition of the phosphorylation of the protein substrate by staurosporine, much more precisely than in Figure 4.
• it is therefore necessary to relate this quantity of modified protein substrate to the total quantity of protein substrate contained in the same sample.
• Example 8 Use of covalent labelling using O(6)-alkylauanine-DNA alkyltransferase (Snaptag) activity to measure the expression and phosphorylation of an Akt protein substrate by co-transfection of the protein substrate and of the enzyme
• This example illustrates the use of the method according to the invention for measuring the level of phosphorylation and the quantity of substrate expressed after co-transfection in the cells of the plasmid coding for the protein substrate and of the plasmid coding for the Akt kinase.
• This example illustrates in particular the use of a suicide enzyme as a coupling domain, in this case O(6)-alkylguanine-DNA alkyltransferase (Snaptag), for labelling the substrate with a coupling agent, in this case a Benzylguanine-Dy647 conjugate as a fluorescent acceptor compound.
• This implementation is an excellent alternative to the use of tag/antitag systems for labelling the substrate by one of the FRET partner components, in this case the Dy647 acceptor.
• the following sequence represents the sense strand (5'-3') coding for a fusion protein comprising: the c-myc tag (underlined), a generic substrate recognized by the serine/threonine kinases (in bold) and the FLAG tag (dotted underlining), flanked in position 5' by part of the restriction site of BamH1 and in position 3' by part of the restriction site of Xho1 :
• the double-strand oligonucleotide is obtained by hybridizing the following two oligomers:
• the sequence is inserted into the pSEMS plasmid (from Covalys) by mixing 1 ⁇ l of Quick T4 DNA ligase (New England Biolabs Cat N° M2200S), 1 ⁇ l of hybridized oligonucleotides and 50 ng of plasmid previously digested with the restriction enzymes BamH1 and Xho1 for 10 min at ambient temperature.
• the plasmid is then incubated with One Shot® TOP10 competent cells (Invitrogen Co ⁇ . Cat N° C4040-06) for 1 hour at 37°C then the cells are plated on plates containing ampicillin.
• HEK293 cells 80000 HEK293 cells (ECACC) are either co-transfected with 31.25 ng of plasmid coding for the substrate and 250 ng Akt1-pcDNA 3.1 (Invitrogen Corp. Cat N° V790-20) or by 280 ng of empty pcDNA3.1 plasmid (Invitrogen Corp. Cat N° V790- 20).
• the co-transfection is carried out in the presence of Lipofectamine 2000 (Invitrogen corp. Cat N° 11668-019) and OPTI-MEM medium (Gibco Cat N° 31985).
• the cells are then cultured for 24h at 37 0 C in 100 ⁇ l of DMEM medium (Gibco Cat N 0 11965-092), to which are added 10% FCS (Hyclone Cat N°SV30014-03) and 1% antibiotic and antifungal (Gibco Cat N° 15240-062) in 96-well assay plates (Cellstar black).
• the cells are lysed in 50 mM Hepes buffer, pH 7, containing 0.1% BSA, 0.4 M potassium fluoride, 1 mM de DTT,1% triton X100, 20 mM EDTA, 1X ser/thre phosphatase inhibitors (sigma) under 50 ⁇ l after aspiration of the 150 ⁇ l transfection medium.
• This same buffer contains 5.4 ng anti-c myc antibody (Cisbio CIS bio international Cat N 0 61 MYCKLA) conjugated with the donor (europium cryptate) and 60 ng anti- FLAG conjugated with the acceptor (cross-linked allophycocyanin, XL 665, CIS bio international Cat N° 61FG2XLA) or increasing quantities (3.12 nM to 100 nM) of benzylguanine BG conjugated with the acceptor BG-Dy647 (Dyomics GmbH) to measure the level of expression of the substrate.
• the plate is incubated for up to 2Oh at ambient temperature before time-resolved reading.
• the FRET signals are measured on a Rubystar at 620 nm (emission wavelength of rare earth cryptate) and 665 nm (emission wavelength of allophycocyanin and DY647) after excitation by a laser at 330 nm.
• the ratio between the fluorescence emitted at 665 nm (fluorescence of the acceptor) and the fluorescence emitted at 620 nm (fluorescence of the donor) (Ratio 665/620) is representative of the FRET occurring between the donor (europium cryptate) and the acceptor (Allophycocyanin Dy647). This FRET is proportional to the spatial proximity between the donor and the acceptor.
• the delta F (%) (DF) corresponds to: (Ratio 665/620 of the sample x 10000)- (Ratio 665/620 of the negative control x 10000) X100
• the negative control signal corresponds to the signal obtained with the cells transfected by an empty pcDNA3.1 plasmid.
• the cells are transfected with the empty plasmid pcDNA3.1 or co-transfected by the plasmids coding for the substrate and the Akt kinase. After lysis of the cells, the level of expression and the phosphorylation of the substrate are detected by using:

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