EP1590772A1 - Method for high-resolution 3d reconstruction - Google Patents

Method for high-resolution 3d reconstruction

Info

Publication number
EP1590772A1
EP1590772A1 EP04704378A EP04704378A EP1590772A1 EP 1590772 A1 EP1590772 A1 EP 1590772A1 EP 04704378 A EP04704378 A EP 04704378A EP 04704378 A EP04704378 A EP 04704378A EP 1590772 A1 EP1590772 A1 EP 1590772A1
Authority
EP
European Patent Office
Prior art keywords
crystal
reconstruction
space group
sample
microcrystals
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP04704378A
Other languages
German (de)
French (fr)
Inventor
Ulf Skoglund
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Sidec Technologies AB
Original Assignee
Sidec Technologies AB
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from SE0300223A external-priority patent/SE526941C2/en
Application filed by Sidec Technologies AB filed Critical Sidec Technologies AB
Publication of EP1590772A1 publication Critical patent/EP1590772A1/en
Withdrawn legal-status Critical Current

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C30—CRYSTAL GROWTH
    • C30B—SINGLE-CRYSTAL GROWTH; UNIDIRECTIONAL SOLIDIFICATION OF EUTECTIC MATERIAL OR UNIDIRECTIONAL DEMIXING OF EUTECTOID MATERIAL; REFINING BY ZONE-MELTING OF MATERIAL; PRODUCTION OF A HOMOGENEOUS POLYCRYSTALLINE MATERIAL WITH DEFINED STRUCTURE; SINGLE CRYSTALS OR HOMOGENEOUS POLYCRYSTALLINE MATERIAL WITH DEFINED STRUCTURE; AFTER-TREATMENT OF SINGLE CRYSTALS OR A HOMOGENEOUS POLYCRYSTALLINE MATERIAL WITH DEFINED STRUCTURE; APPARATUS THEREFOR
    • C30B35/00—Apparatus not otherwise provided for, specially adapted for the growth, production or after-treatment of single crystals or of a homogeneous polycrystalline material with defined structure

Definitions

  • the present invention relates to a method for achieving a high-resolution 3D reconstruction of a crystal as defined in the preamble of claim 1.
  • the macromolecules are often grown into crystals first.
  • the crystals must be relatively large, typically in the order of magnitude of lO ⁇ m. Such crystals are referred to as macrocrystals.
  • the state of the art procedure for growing crystals is as follows: A buffer solution of the molecule that is to be crystallized is placed in a petri dish, either as a hanging drop or as a sitting drop, surrounded by a similar solution having a higher concentration of e.g. salt. Because of the different concentrations, the solution in the hanging drop or sitting drop will then evaporate, causing a precipitation in the drop comprising a higher concentration of the molecule.
  • the molecule may or may not have crystallized depending on the conditions. The conditions favouring crystallization are not the same for different types of molecules, which means that each type of molecule must be tried out individually.
  • the crystals formed range from very small to, in the best case, some that are large enough to be used.
  • FB filtered backprojection
  • Comet technology as described in the International Patent Application W097/33255, hereby incorporated by reference, (corresponding European Patent Application EP 885 430 and Swedish Patent Application 9601229-9) is used for image reconstruction.
  • the Comet technology is based on the following steps: An initial estimated distribution of the sample is provided
  • a blurred prior prejudice distribution is provided based on the estimated distribution Observed data of the sample is provided
  • a calculating means calculates, for each iteration, a new estimated distribution of the sample using a comparison between the estimated distribution and the observed data of the sample. A new prior prejudice distribution less blurred than the previous one is also calculated. The iterations are continued until the difference between the new estimated distribution and the next preceding estimated distribution is less than a predetermined condition.
  • the repetitive structure of the crystal and, if possible, the space group of the crystal is determined.
  • the geometry is refined and a second 3D reconstruction, using a procedure as described above, for example the combination of filtered backprojection and COMET, is obtained including information about the space group.
  • Information about the quality of the sample can also be used as feedback for the process of growing crystals.
  • the method according to the invention enables the use of microcrystals for achieving 3D reconstructions with a very high resolution, in the order of magnitude of lOA.
  • a major advantage of the method is that molecules that have been modified can be identified and analyzed. Generally, even if a molecule can be crystallized, a small modification such as the addition of a ligand can make it difficult or impossible to crystallize it into macrocrystals. Studies of how ligands are bound to a certain protein are of great interest to protein chemists and with the inventive method this can be studied down to the level of which amino acid the ligand is bound to. The structures can also be compared to protein structures that have already been determined. With the inventive method, therefore, a more flexible handling of ligands is enabled.
  • the inventive method will also enable 3D reconstructions to be made of entirely new types of molecules, like proteoglycans.
  • the samples are examined to see which ones are likely to have any crystals at all. This can be done by looking at them, first with the bare eye or with a light microscope, then for example through a Transmission Electron Microscope (TEM).
  • TEM Transmission Electron Microscope
  • a sample that comprises crystals is selected (S2) and treated as follows: First it is subjected to a process, for example spinning (S3), to crush the crystals into very small crystals, microcrystals, in the order of magnitude of lOOnm. These microcrystals can be treated in the same way as for proteins in a solution to vitrify them for cryo-TEM (S4), that is Place a thin film of the solution comprising the microcrystals on a grid and plunge-freeze it
  • the crystal fragment is identified and analyzed (S7). If it is of poor quality it is discarded (S9) and the process starts again with another sample.
  • the information that the sample is of poor quality can be used as feedback to exclude the conditions under which the sample was placed, and which were not good for growing crystals.
  • the procedure continues as follows:
  • the information about the sample quality can be used as feedback to adjust the conditions used to grow it so that larger crystals can be grown. More importantly for the inventive process, the repetitive structure of the crystal is determined and its space group, if possible (S10).
  • correlation averaging is performed (SI 2) on the repetitive fragments and the regularity of the lattice of the crystal is estimated. This enables an assessment of the quality and also preliminary information about the 3D structure.
  • the process continues as follows: The geometry of the space group is refined, and its orientation is determined (SI 3). Imaging (SI 4) using the methods as discussed above including space group symmetry. This results in a 3D reconstruction having a very high resolution, probably of the same order of magnitude as what can be achieved for macrocrystals using prior art methods. How to do this for an icosahedral structure has already been described in the International Patent Application W097/33255, hereby incorporated by reference, (corresponding European Patent Application EP 885 430 and Swedish Patent Application 9601229-9).

Abstract

Abstract A method for achieving a high-resolution 3D reconstruction of a crystal, comprising the step of growing a crystal in a way known in the art characterized by the steps of Crushing the crystal into microcrystals, vitrifying a sample of the microcrystals for cryoTEM, recording a tilt series, and obtaining a first 3D reconstruction using the FB+COMET procedure. If the sample is of high quality, the repetitive structure and, if possible, the space group of the crystal are determined. If the space group could be determined, a second 3D reconstruction may be obtained including information about the space group. The method according to the iAbstract A method for achieving a high-resolution 3D reconstruction of a crystal, comprising the step of growing a crystal in a way known in the art characterized by the steps of Crushing the crystal into microcrystals, vitrifying a sample of the microcrystals for cryoTEM, recording a tilt series, and obtaining a first 3D reconstruction using the FB+COMET procedure. If the sample is of high quality, the repetitive structure and, if possible, the space group of the crystal are determined. If the space group could be determined, a second 3D reconstruction may be obtained including information about the space group. The method according to the invention enables the use of microcrystals for achieving 3D reconstructions with a very high resolution, in the order of magnitude of 10Å.

Description

Method for high-resolution 3D reconstruction
Technical Field of the Invention The present invention relates to a method for achieving a high-resolution 3D reconstruction of a crystal as defined in the preamble of claim 1.
Background and Related Art
For the study of proteins and other large molecules by X-ray or neutron crystallog- raphy, the macromolecules are often grown into crystals first. The crystals must be relatively large, typically in the order of magnitude of lOμm. Such crystals are referred to as macrocrystals.
It is difficult to achieve crystals of the required size. Only a small amount of the proteins can be expected to yield crystals that can be grown into large crystals at all, and for those who can, the process involves a lot of trial and error. The state of the art procedure for growing crystals is as follows: A buffer solution of the molecule that is to be crystallized is placed in a petri dish, either as a hanging drop or as a sitting drop, surrounded by a similar solution having a higher concentration of e.g. salt. Because of the different concentrations, the solution in the hanging drop or sitting drop will then evaporate, causing a precipitation in the drop comprising a higher concentration of the molecule. The molecule may or may not have crystallized depending on the conditions. The conditions favouring crystallization are not the same for different types of molecules, which means that each type of molecule must be tried out individually.
Usually a large number of samples are made and placed under different conditions, for example, different surrounding solutions, low temperature, high temperature, varying temperature, varying pH and ionic strength, hoping that some of the condi- tions will be favourable for growing crystals. In subsequent steps conditions that lead to the formation of microcrystals (small crystals much less than about 10 mi- crometers) are adjusted and refined to obtain macrocrystals which can be used for imaging by X-ray and neutron crystallographic techniques.
The crystals formed range from very small to, in the best case, some that are large enough to be used. The samples that do not result in sufficiently large crystals, typically the majority of samples, are discarded.
Object of the Invention
Thus it is an object of the invention to enable the use of a larger fraction of the sam- pies for imaging.
Summary of the Invention
This is achieved according to the invention by a method for achieving a high- resolution 3D reconstruction of a crystal, comprising the step of growing a crystal in a way known in the art characterized by the steps of Crushing the crystal into microcrystals
Nitrifying a sample of the microcrystals for cryoTEM (Transmission Electron Microscopy) Recording a tilt series Obtaining a first 3D reconstruction using an iterative reconstruction method in which a prior prejudice distribution is refined in at least one step on the basis of a comparison with the collected image information
One such method would be to use filtered backprojection (FB) software, or some other fast procedure to get an initial estimate of the 3D structure, followed by an refinement procedure that will result in a high resolution 3D structure. Preferably, after the FB procedure the Comet technology, as described in the International Patent Application W097/33255, hereby incorporated by reference, (corresponding European Patent Application EP 885 430 and Swedish Patent Application 9601229-9) is used for image reconstruction. The Comet technology is based on the following steps: An initial estimated distribution of the sample is provided
A blurred prior prejudice distribution is provided based on the estimated distribution Observed data of the sample is provided
In an iterative process a calculating means calculates, for each iteration, a new estimated distribution of the sample using a comparison between the estimated distribution and the observed data of the sample. A new prior prejudice distribution less blurred than the previous one is also calculated. The iterations are continued until the difference between the new estimated distribution and the next preceding estimated distribution is less than a predetermined condition.
If the sample is of high quality, the repetitive structure of the crystal and, if possible, the space group of the crystal is determined.
If the space group could be determined, the geometry is refined and a second 3D reconstruction, using a procedure as described above, for example the combination of filtered backprojection and COMET, is obtained including information about the space group.
If the space group could not be determined, perform correlation averaging on the sample.
Information about the quality of the sample can also be used as feedback for the process of growing crystals.
The method according to the invention enables the use of microcrystals for achieving 3D reconstructions with a very high resolution, in the order of magnitude of lOA. This in turn means that such 3D reconstructions can be made for molecules that cannot be imaged by X-ray or neutron crystallographic techniques today because it has been impossible to grow large enough crystals for state of the art methods. Only a small amount of the macromolecules cannot be grown to microcrystals. In con- trast, as mentioned above, only a minor portion can be grown to macrocrystals.
A major advantage of the method is that molecules that have been modified can be identified and analyzed. Generally, even if a molecule can be crystallized, a small modification such as the addition of a ligand can make it difficult or impossible to crystallize it into macrocrystals. Studies of how ligands are bound to a certain protein are of great interest to protein chemists and with the inventive method this can be studied down to the level of which amino acid the ligand is bound to. The structures can also be compared to protein structures that have already been determined. With the inventive method, therefore, a more flexible handling of ligands is enabled.
The inventive method will also enable 3D reconstructions to be made of entirely new types of molecules, like proteoglycans.
Brief Description of the Drawing In the following the invention will be described in more detail, with reference to the appended Figure 1, which is an overall flow chart of the inventive method.
Detailed Description
According to the invention, when the preparatory process to grow crystals (SI) de- scribed initially is over, first the samples are examined to see which ones are likely to have any crystals at all. This can be done by looking at them, first with the bare eye or with a light microscope, then for example through a Transmission Electron Microscope (TEM).
A sample that comprises crystals is selected (S2) and treated as follows: First it is subjected to a process, for example spinning (S3), to crush the crystals into very small crystals, microcrystals, in the order of magnitude of lOOnm. These microcrystals can be treated in the same way as for proteins in a solution to vitrify them for cryo-TEM (S4), that is Place a thin film of the solution comprising the microcrystals on a grid and plunge-freeze it
Record a standard cryo-TEM tilt series for the ensuing 3D reconstruction.. Align with, for example, gold markers Generate a 3D reconstruction (S6) using an iterative reconstruction method in which a prior prejudice distribution is refined in at least one step on the basis of a comparison with the collected image information, for example the combination of filtered backprojection and COMET as discussed above. This involves first taking a back- projection or getting an estimate of the structure in an alternative way before imaging using the iterative method. This results in information about the structure of the crystal fragment.
Next the crystal fragment is identified and analyzed (S7). If it is of poor quality it is discarded (S9) and the process starts again with another sample. The information that the sample is of poor quality can be used as feedback to exclude the conditions under which the sample was placed, and which were not good for growing crystals.
If the crystal fragment is of good quality, the procedure continues as follows: The information about the sample quality can be used as feedback to adjust the conditions used to grow it so that larger crystals can be grown. More importantly for the inventive process, the repetitive structure of the crystal is determined and its space group, if possible (S10).
If the space group cannot be determined correlation averaging is performed (SI 2) on the repetitive fragments and the regularity of the lattice of the crystal is estimated. This enables an assessment of the quality and also preliminary information about the 3D structure.
If the space group can be determined the process continues as follows: The geometry of the space group is refined, and its orientation is determined (SI 3). Imaging (SI 4) using the methods as discussed above including space group symmetry. This results in a 3D reconstruction having a very high resolution, probably of the same order of magnitude as what can be achieved for macrocrystals using prior art methods. How to do this for an icosahedral structure has already been described in the International Patent Application W097/33255, hereby incorporated by reference, (corresponding European Patent Application EP 885 430 and Swedish Patent Application 9601229-9). All symmetry groups, crystallographic as well as non- crystallographic can be readily implemented in the COMET procedure using the methods disclosed in this document since it only concerns averaging of the gradient maps in the search directions. In the example given in the reference the icosahedral symmetry was used in the refinement of the adeno virus structure by averaging the two search directions of the 3D gradient density maps of the chi-square and entropy functions. The averaging then precisely followed the specification for the specified symmetry group. The skilled person will realize that the COMET proce- dure can be applied to any kind of symmetry operator and should be implemented in an analogous way to the example referred to above.

Claims

Claims
1. A method for achieving a high-resolution 3D reconstruction of a crystal, comprising the step of growing a crystal in a way known in the art characterized by the steps of Crushing the crystal into microcrystals
Nitrifying a sample of the microcrystals for cryoTEM Recording a tilt series
Obtaining a first 3D reconstruction using an iterative reconstruction method in which a prior prejudice distribution is refined in at least one step on the basis of a comparison with the collected image information
2. A method according to claim 1, wherein the iterative reconstruction method is the a filtered backprojection followed by the COMET procedure
3. A method according to claim 2, further comprising the step of: if the sample is of high quality, determining the repetitive structure of the crystal and, if possible, the space group of the crystal.
4. A method according to claim 3, further comprising the following steps: If the space group could be determined, refine the geometry and obtain a second 3D reconstruction including information about the space group.
5. A method according to claim 4, further comprising the following step: if the space group could not be determined, perform correlation averaging on the sample.
EP04704378A 2003-01-30 2004-01-22 Method for high-resolution 3d reconstruction Withdrawn EP1590772A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US31991503P 2003-01-30 2003-01-30
US319915P 2003-01-30
SE0300223A SE526941C2 (en) 2003-01-30 2003-01-30 High resolution 3D reproduction procedure
SE0300223 2003-01-30
PCT/SE2004/000075 WO2004068415A1 (en) 2003-01-30 2004-01-22 Method for high-resolution 3d reconstruction

Publications (1)

Publication Number Publication Date
EP1590772A1 true EP1590772A1 (en) 2005-11-02

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EP04704378A Withdrawn EP1590772A1 (en) 2003-01-30 2004-01-22 Method for high-resolution 3d reconstruction

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EP (1) EP1590772A1 (en)
JP (1) JP2006517667A (en)
WO (1) WO2004068415A1 (en)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2002246A1 (en) 2006-04-04 2008-12-17 Sidec Technologies AB Extended electron tomography
WO2009070120A1 (en) * 2007-11-30 2009-06-04 Sidec Technologies Ab Lp-regularization of sparse representations applied to structure determination methods in molecular biology/structural chemistry
WO2014141630A1 (en) 2013-03-13 2014-09-18 Okinawa Institute Of Science And Technology School Corporation Extended field iterative reconstruction technique (efirt) for correlated noise removal

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
FR2656129B1 (en) * 1989-12-20 1992-03-13 Gen Electric Cgr METHOD FOR MULTI-SCALE RECONSTRUCTION OF THE IMAGE OF THE STRUCTURE OF A BODY.
US5400255A (en) * 1994-02-14 1995-03-21 General Electric Company Reconstruction of images from cone beam data
SE9601229D0 (en) * 1996-03-07 1996-03-29 B Ulf Skoglund Apparatus and method for providing reconstruction
US6507633B1 (en) * 2001-02-15 2003-01-14 The Regents Of The University Of Michigan Method for statistically reconstructing a polyenergetic X-ray computed tomography image and image reconstructor apparatus utilizing the method
SE0100728D0 (en) * 2001-03-05 2001-03-05 Sidec Technologies Ab Karolins New method

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
SKOGLUND U. ET AL: "Maximum-Entropy Three-Dimensional Reconstruction with Deconvolution of the Contrast Transfer Function: A Test Application with Adenovirus", vol. 117, 1996, pages 173 - 188 *

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JP2006517667A (en) 2006-07-27
WO2004068415A1 (en) 2004-08-12

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