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PMID: 18441029 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Review

Determination of protein structures--a series of fortunate events.

Biophysical journal ·Vol. 95 ·No. 1 ·2008-07-00 ·Pages 1-9

Chruszcz M, Wlodawer A, Minor W

Abstract

Determination of a macromolecular structure using x-ray diffraction is a multistep process that involves a plethora of techniques involving molecular biology, bioinformatics, and physical sciences. Counterintuitively, the success of any or all individual steps does not guarantee the success of the overall process. This review examines the difficulties presented by each step on the path from a gene to the final publication, together with certain lucky (or unlucky) circumstances that can affect the velocity along that path.

MeSH Terms
Computer Simulation Crystallography/methods Models, Chemical Models, Molecular Protein Conformation Proteins/chemistry,ultrastructure
Chemicals
Proteins
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Chruszcz Maksymilian
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA.
Wlodawer Alexander
Minor Wladek
References (64)
64 references, click to expand
  1. Numerology.
    Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):275 PMID: 17327662
  2. New vectors for co-expression of proteins: structure of Bacillus subtilis ScoAB obtained by high-throughput protocols.
    Protein Expr Purif. 2007 Jun;53(2):396-403 PMID: 17363272
  3. Atomic-resolution crystal structure of the proteolytic domain of Archaeoglobus fulgidus lon reveals the conformational variability in the active sites of lon proteases.
    J Mol Biol. 2005 Aug 5;351(1):144-57 PMID: 16002085
  4. Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices.
    Biochemistry. 2007 May 15;46(19):5722-31 PMID: 17441732
  5. Chelating peptide-immobilized metal ion affinity chromatography. A new concept in affinity chromatography for recombinant proteins.
    J Biol Chem. 1988 May 25;263(15):7211-5 PMID: 3284883
  6. Improved methods for building protein models in electron density maps and the location of errors in these models.
    Acta Crystallogr A. 1991 Mar 1;47 ( Pt 2):110-9 PMID: 2025413
  7. Towards rationalization of crystallization screening for small- to medium-sized academic laboratories: the PACT/JCSG+ strategy.
    Acta Crystallogr D Biol Crystallogr. 2005 Oct;61(Pt 10):1426-31 PMID: 16204897
  8. The impact of structural genomics: expectations and outcomes.
    Science. 2006 Jan 20;311(5759):347-51 PMID: 16424331
  9. Radiation damage in protein crystallography.
    J Mol Biol. 1976 Sep 25;106(3):889-93 PMID: 978739
  10. The architecture of metal coordination groups in proteins.
    Acta Crystallogr D Biol Crystallogr. 2004 May;60(Pt 5):849-59 PMID: 15103130
  11. Crystal structure of Escherichia coli L-asparaginase, an enzyme used in cancer therapy.
    Proc Natl Acad Sci U S A. 1993 Feb 15;90(4):1474-8 PMID: 8434007
  12. The CCP4 suite: programs for protein crystallography.
    Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3 PMID: 15299374
  13. Glycoprotein structural genomics: solving the glycosylation problem.
    Structure. 2007 Mar;15(3):267-73 PMID: 17355862
  14. Errors in protein structures.
    Nature. 1996 May 23;381(6580):272 PMID: 8692262
  15. The use of recombinant methods and molecular engineering in protein crystallization.
    Methods. 2004 Nov;34(3):354-63 PMID: 15325653
  16. His-tag impact on structure.
    Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):295-301 PMID: 17327666
  17. Catalysis of protein folding by an immobilized small-molecule dithiol.
    Biotechnol Prog. 2003 Jul-Aug;19(4):1307-14 PMID: 12892495
  18. Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis.
    Nature. 1960 Feb 13;185(4711):416-22 PMID: 18990801
  19. Studies of two crystal forms of L-glutaminase-asparaginase from Acinetobacter glutaminasificans.
    J Mol Biol. 1975 Dec 5;99(2):295-9 PMID: 1206706
  20. The structural genomics experimental pipeline: insights from global target lists.
    Proteins. 2004 Aug 1;56(2):201-10 PMID: 15211505
  21. Comparison of four independently determined structures of human recombinant interleukin-4.
    Nat Struct Biol. 1994 May;1(5):301-10 PMID: 7664036
  22. SOLVE and RESOLVE: automated structure solution, density modification and model building.
    J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):49-52 PMID: 14646132
  23. Catalysis in the crystal: synchrotron radiation studies with glycogen phosphorylase b.
    EMBO J. 1987 Feb;6(2):539-46 PMID: 3107984
  24. Identifying protein construct variants with increased crystallization propensity--a case study.
    Protein Sci. 2006 Dec;15(12):2718-28 PMID: 17132859
  25. Refinement of macromolecular structures by the maximum-likelihood method.
    Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55 PMID: 15299926
  26. An unfolding/refolding step helps in the crystallization of a poorly soluble protein.
    Acta Crystallogr D Biol Crystallogr. 2003 Jul;59(Pt 7):1243-5 PMID: 12832773
  27. Crystallography & NMR system: A new software suite for macromolecular structure determination.
    Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21 PMID: 9757107
  28. Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?
    Acta Crystallogr D Biol Crystallogr. 2007 May;63(Pt 5):611-20 PMID: 17452786
  29. DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis.
    Nucleic Acids Res. 2002 May 15;30(10):e43 PMID: 12000848
  30. Solubility of proteins isolated from inclusion bodies is enhanced by fusion to maltose-binding protein or thioredoxin.
    Protein Expr Purif. 1998 Feb;12(1):122-32 PMID: 9473466
  31. Structure validation by Calpha geometry: phi,psi and Cbeta deviation.
    Proteins. 2003 Feb 15;50(3):437-50 PMID: 12557186
  32. Lysine methylation as a routine rescue strategy for protein crystallization.
    Structure. 2006 Nov;14(11):1617-22 PMID: 17098187
  33. Intensity statistics in twinned crystals with examples from the PDB.
    Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):83-95 PMID: 16369097
  34. Crystal structure of a transcriptional regulator TM1030 from Thermotoga maritima solved by an unusual MAD experiment.
    J Struct Biol. 2007 Sep;159(3):424-32 PMID: 17588774
  35. SHELXL: high-resolution refinement.
    Methods Enzymol. 1997;277:319-43 PMID: 18488315
  36. Crystal structure of the N-terminal domain of E. coli Lon protease.
    Protein Sci. 2005 Nov;14(11):2895-900 PMID: 16199667
  37. Entropy and surface engineering in protein crystallization.
    Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):116-24 PMID: 16369101
  38. Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals.
    Protein Sci. 2003 Sep;12(9):1865-71 PMID: 12930986
  39. Metal chelate affinity chromatography, a new approach to protein fractionation.
    Nature. 1975 Dec 18;258(5536):598-9 PMID: 1678
  40. Searching for silver bullets: an alternative strategy for crystallizing macromolecules.
    J Struct Biol. 2006 Dec;156(3):387-406 PMID: 17101277
  41. HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes.
    Acta Crystallogr D Biol Crystallogr. 2006 Aug;62(Pt 8):859-66 PMID: 16855301
  42. Coot: model-building tools for molecular graphics.
    Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32 PMID: 15572765
  43. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.
    Science. 2000 Aug 11;289(5481):905-20 PMID: 10937989
  44. Crystallization of nerve growth factor from mouse submaxillary glands.
    Proc Natl Acad Sci U S A. 1975 Mar;72(3):777-9 PMID: 1055377
  45. PHENIX: building new software for automated crystallographic structure determination.
    Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54 PMID: 12393927
  46. Parameters for crystal growth of ribosomal subunits.
    J Cell Biochem. 1982;19(2):145-55 PMID: 7174745
  47. An expression vector tailored for large-scale, high-throughput purification of recombinant proteins.
    Protein Expr Purif. 2006 Jun;47(2):446-54 PMID: 16497515
  48. Slicing a protease: structural features of the ATP-dependent Lon proteases gleaned from investigations of isolated domains.
    Protein Sci. 2006 Aug;15(8):1815-28 PMID: 16877706
  49. Cryocrystallography of macromolecules: practice and optimization.
    Methods Mol Biol. 2007;364:1-18 PMID: 17172757
  50. Deposition of structural data redux.
    Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):421-3 PMID: 17327681
  51. New protein fold revealed by a 2.3-A resolution crystal structure of nerve growth factor.
    Nature. 1991 Dec 5;354(6352):411-4 PMID: 1956407
  52. The well-tempered protein crystal: annealing macromolecular crystals.
    Methods Enzymol. 2003;368:217-35 PMID: 14674276
  53. Intrinsic protein disorder in complete genomes.
    Genome Inform Ser Workshop Genome Inform. 2000;11:161-71 PMID: 11700597
  54. Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures.
    FEBS J. 2008 Jan;275(1):1-21 PMID: 18034855
  55. The active site of a lon protease from Methanococcus jannaschii distinctly differs from the canonical catalytic Dyad of Lon proteases.
    J Biol Chem. 2004 Dec 17;279(51):53451-7 PMID: 15456757
  56. Comparison of three commercial sparse-matrix crystallization screens.
    Acta Crystallogr D Biol Crystallogr. 2003 Apr;59(Pt 4):769-72 PMID: 12657807
  57. Predicting protein disorder and induced folding: from theoretical principles to practical applications.
    Curr Protein Pept Sci. 2007 Apr;8(2):135-49 PMID: 17430195
  58. Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins.
    Proc Natl Acad Sci U S A. 2006 Dec 19;103(51):19243-8 PMID: 17159147
  59. Effect of osmotic stress and heat shock in recombinant protein overexpression and crystallization.
    Protein Expr Purif. 2007 Apr;52(2):280-5 PMID: 17126029
  60. Quantitative analysis in the characterization and optimization of protein crystal growth.
    Acta Crystallogr D Biol Crystallogr. 1994 Jul 1;50(Pt 4):572-90 PMID: 15299421
  61. In situ proteolysis for protein crystallization and structure determination.
    Nat Methods. 2007 Dec;4(12):1019-21 PMID: 17982461
  62. Automated protein model building combined with iterative structure refinement.
    Nat Struct Biol. 1999 May;6(5):458-63 PMID: 10331874
  63. A survey of protein-protein complex crystallizations.
    Acta Crystallogr D Biol Crystallogr. 2006 Jun;62(Pt 6):605-12 PMID: 16699187
  64. The protein as a variable in protein crystallization.
    J Struct Biol. 2003 Apr;142(1):88-97 PMID: 12718922
Article Info
Journal
Biophysical journal
Abbr.
Biophys J
ISSN
1542-0086
DOI
10.1529/biophysj.108.131789
Published
2008-07-00
Epub
2008-00-25
Pages
1-9
Language
English
Region
United States
NLM ID
0370626
PMCID
PMC2426657
Subset
IM
Grants
NIGMS NIH HHS · GM53163 · United States
NIGMS NIH HHS · R01 GM053163 · United States
Intramural NIH HHS · United States
NIGMS NIH HHS · GM74942 · United States
NIGMS NIH HHS · U54 GM074942 · United States
External Links
PubMed source DOI: 10.1529/biophysj.108.131789 PMC Full Text View journal details
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