Protein Structure Fitting and Refinement Guided by Cryo-EM Density

Structure

Volumn 16, Issue 2, 2008, Pages 295-307

  Topf, Maya ^a   Lasker, Keren ^b,c   Webb, Ben ^b   Wolfson, Haim ^c   Chiu, Wah ^d   Sali, Andrej ^b  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

^d BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

PROTEINS

Indexed keywords

ARTICLE; CRYOELECTRON MICROSCOPY; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STRUCTURE; SCORING SYSTEM; STEREOCHEMISTRY;

CRYOELECTRON MICROSCOPY; GROEL PROTEIN; MODELS, MOLECULAR; MONTE CARLO METHOD; PEPTIDE ELONGATION FACTOR TU; PROTEIN STRUCTURE, TERTIARY;

EID: 38949092920     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2007.11.016     Document Type: Article

References (54)

1. Alber F., Eswar N., and Sali A. Structure determination of macromolecular complexes by experiment and computation. In: Bujnicki J. (Ed). Practical Bioinformatics, Volume 15 (2004), Springer-Verlag, Berlin and Heidelberg 73-96
2. Alexandrov V., Lehnert U., Echols N., Milburn D., Engelman D., and Gerstein M. Normal modes for predicting protein motions: a comprehensive database assessment and associated web tool. Protein Sci. 14 (2005) 633-643
3. Andersen G.R., Thirup S., Spremulli L.L., and Nyborg J. High resolution crystal structure of bovine mitochondrial EF-Tu in complex with GDP. J. Mol. Biol. 297 (2000) 421-436
4. Bairoch A., Apweiler R., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., et al. The Universal Protein Resource (UniProt). Nucleic Acids Res. 33 (2005) D154-D159
5. Baker D., and Sali A. Protein structure prediction and structural genomics. Science 294 (2001) 93-96
6. Baker M.L., Jiang W., Wedemeyer W.J., Rixon F.J., Baker D., and Chiu W. Ab initio modeling of the herpesvirus VP26 core domain assessed by cryoEM density. PLoS Comput. Biol. 2 (2006) e146
7. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S., Sonnhammer E.L., et al. The Pfam protein families database. Nucleic Acids Res. 32 (2004) D138-D141
8. Braig K., Adams P.D., and Brunger A.T. Conformational variability in the refined structure of the chaperonin GroEL at 2.8 Å resolution. Nat. Struct. Biol. 2 (1995) 1083-1094
9. Brooks B., and Karplus M. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. USA 80 (1983) 6571-6575
10. Brooks C.L., Karplus M., and Pettitt B.M. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics (1988), Wiley, New York and Chichester
11. Chapman M.S. Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function. Acta Crystallogr. A 51 (1995) 69-80
12. Chen J.Z., Furst J., Chapman M.S., and Grigorieff N. Low-resolution structure refinement in electron microscopy. J. Struct. Biol. 144 (2003) 144-151
13. Chen Z., and Champman M.S. Conformational disorder of proteins assessed by real-space molecular dynamics refinement. Biophys. J. 80 (2001) 1466-1472
14. Chiu W., Baker M.L., Jiang W., Dougherty M., and Schmid M.F. Electron cryomicroscopy of biological machines at subnanometer resolution. Structure 13 (2005) 363-372
15. Eswar N., Webb B., Marti-Renom M.A., Madhusudhan M.S., Eramian D., Shen M.Y., Pieper U., and Sali A. Comparative protein structure modeling with MODELLER. Curr. Protoc. Protein Sci. 50 (2007) 2.9.1-2.9.31
16. Fabiola F., and Chapman M.S. Fitting of high-resolution structures into electron microscopy reconstruction images. Structure 13 (2005) 389-400
17. Fiser A., Do R.K., and Sali A. Modeling of loops in protein structures. Protein Sci. 9 (2000) 1753-1773
18. Flores S., Echols N., Milburn D., Hespenheide B., Keating K., Lu J., Wells S., Yu E.Z., Thorpe M., and Gerstein M. The database of macromolecular motions: new features added at the decade mark. Nucleic Acids Res. 34 (2006) D296-D301
19. Flores S.C., and Gerstein M.B. FlexOracle: predicting flexible hinges by identification of stable domains. BMC Bioinformatics 8 (2007) 215
20. Goddard T.D., Huang C.C., and Ferrin T.E. Visualizing density maps with UCSF Chimera. J. Struct. Biol. 157 (2007) 281-287
21. Goldstein H. Classical Mechanics. Second Edition (1980), Addison-Wesley, Reading, MA
22. Han J.H., Kerrison N., Chothia C., and Teichmann S.A. Divergence of interdomain geometry in two-domain proteins. Structure 14 (2006) 935-945
23. Jiang W., and Ludtke S.J. Electron cryomicroscopy of single particles at subnanometer resolution. Curr. Opin. Struct. Biol. 15 (2005) 571-577
24. John B., and Sali A. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res. 31 (2003) 3982-3992
25. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
26. Lovell S.C., Davis I.W., Adrendall W.B., de Bakker P.I.W., Word J.M., Prisant M.G., Richardson J.S., and Richardson D.C. Structure validation by C α geometry: φ{symbol},ψ and C β deviation. Proteins Struct. Funct. Genet. 50 (2003) 437-450
27. Ludtke S.J., Jakana J., Song J.L., Chuang D.T., and Chiu W. A 11.5 Å single particle reconstruction of GroEL using EMAN. J. Mol. Biol. 314 (2001) 253-262
28. Ludtke S.J., Chen D.H., Song J.L., Chuang D.T., and Chiu W. Seeing GroEL at 6 Å resolution by single particle electron cryomicroscopy. Structure 12 (2004) 1129-1136
29. Ma J. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 13 (2005) 373-380
30. MacKerell Jr. A.D., Bashford D., Bellott M., Dunbrack Jr. R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102 (1998) 3586-3616
31. Marti-Renom M.A., Pieper U., Madhusudhan M.S., Rossi A., Eswar N., Davis F.P., Al-Shahrour F., Dopazo J., and Sali A. DBAli tools: mining the protein structure space. Nucleic Acids Res. 35 (2007) W393-W397
32. Ming D., Kong Y., Wakil S.J., Brink J., and Ma J. Domain movements in human fatty acid synthase by quantized elastic deformational model. Proc. Natl. Acad. Sci. USA 99 (2002) 7895-7899
33. Mitra K., and Frank J. Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Annu. Rev. Biophys. Biomol. Struct. 35 (2006) 299-317
34. Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
35. Petrone P., and Pande V.S. Can conformational change be described by only a few normal modes?. Biophys. J. 90 (2006) 1583-1593
36. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., and Ferrin T.E. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25 (2004) 1605-1612
37. Pieper U., Eswar N., Davis F.P., Braberg H., Madhusudhan M.S., Rossi A., Marti-Renom M., Karchin R., Webb B.M., Eramian D., et al. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 34 (2006) D291-D295
38. Rossmann M.G., Morais M.C., Leiman P.G., and Zhang W. Combining X-ray crystallography and electron microscopy. Structure 13 (2005) 355-362
39. Russell R.B., Alber F., Aloy P., Davis F.P., Korkin D., Pichaud M., Topf M., and Sali A. A structural perspective on protein-protein interactions. Curr. Opin. Struct. Biol. 14 (2004) 313-324
40. Saibil H.R. Conformational changes studied by cryo-electron microscopy. Nat. Struct. Biol. 7 (2000) 711-714
41. Sali A., and Blundell T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234 (1993) 779-815
42. Sali A., Glaeser R., Earnest T., and Baumeister W. From words to literature in structural proteomics. Nature 422 (2003) 216-225
43. Shanno D.F., and Phua K.H. Remark on algorithm 500. Minimization of unconstrained multivariate functions. Trans. Math. Softw. 6 (1980) 618-622
44. Shen M.Y., and Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 15 (2006) 2507-2524
45. Shimamura T., Koike-Takeshita A., Yokoyama K., Masui R., Murai N., Yoshida M., Taguchi H., and Iwata S. Crystal structure of the native chaperonin complex from Thermus thermophilus revealed unexpected asymmetry at the cis-cavity. Structure 12 (2004) 1471-1480
46. Suhre K., Navaza J., and Sanejouand Y.H. NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps. Acta Crystallogr. D Biol. Crystallogr. 62 (2006) 1098-1100
47. Tama F., Wriggers W., and Brooks III C.L. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J. Mol. Biol. 321 (2002) 297-305
48. Tama F., Miyashita O., and Brooks III C.L. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J. Mol. Biol. 337 (2004) 985-999
49. Topf M., and Sali A. Combining electron microscopy and comparative protein structure modeling. Curr. Opin. Struct. Biol. 15 (2005) 578-585
50. Topf M., Baker M.L., John B., Chiu W., and Sali A. Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J. Struct. Biol. 149 (2005) 191-203
51. Topf M., Baker M.L., Marti-Renom M.A., Chiu W., and Sali A. Refinement of protein structures by iterative comparative modeling and cryoEM density fitting. J. Mol. Biol. 357 (2006) 1655-1668
52. Valle M., Zavialov A., Li W., Stagg S.M., Sengupta J., Nielsen R.C., Nissen P., Harvey S.C., Ehrenberg M., and Frank J. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat. Struct. Biol. 10 (2003) 899-906
53. Velazquez-Muriel J.A., Valle M., Santamaria-Pang A., Kakadiaris I.A., and Carazo J.M. Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies. Structure 14 (2006) 1115-1126
54. Wriggers W., Milligan R.A., and McCammon J.A. Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 125 (1999) 185-195