Mega-Dalton biomolecular motion captured from electron microscopy reconstructions

Journal of Molecular Biology

Volumn 326, Issue 2, 2003, Pages 485-492

  Chacón, Pablo ^a   Tama, Florence ^a   Wriggers, Willy ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Domain motions; Flexing; Macromolecular assemblies; Normal mode analysis; Subcellular machines

Indexed keywords

BACTERIAL ENZYME; CHAPERONIN; RNA POLYMERASE;

ARTICLE; ATOM; CELL MOTION; CONTROLLED STUDY; ELASTICITY; ELECTRON MICROSCOPY; ESCHERICHIA COLI; EXTRACTION; IMAGE RECONSTRUCTION; MACROMOLECULE; MOLECULAR INTERACTION; MOTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; RIBOSOME SUBUNIT; VIBRATION;

BACTERIA (MICROORGANISMS);

EID: 0037436340     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)01426-2     Document Type: Article

References (40)

1. Gerstein M., Lesk A.M., Chothia C. Structural mechanisms for domain movements in proteins. Biochemistry. 33:1994;6739-6749.
2. Alberts B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell. 92:1998;291-294.
3. Frank J. Three-Dimensional Electron Microscopy of Macromolecular Assemblies. 1996;Academic Press, San Diego.
4. Packer M.J., Hunter C.A. Sequence dependent DNA structure: the role of the sugar phosphate backbone. J. Mol. Biol. 280:1998;407-420.
5. McCammon J.A., Harvey S.C. Dynamics of Proteins and Nucleic Acids. 1987;Cambridge University Press, Cambridge.
6. Leach A.R. Molecular Modelling: Principles and Applications. 1996;Addison Wesley Longman, Essex, UK.
7. Clarage J.B., Romo T., Andrews B.K., Pettitt B.M., Phillips G.N. A sampling problem in molecular dynamics simulations of macromolecules. Proc. Natl Acad. Sci. USA. 92:1995;3288-3292.
8. Balsera M.A., Wriggers W., Oono Y., Schulten K. Principal component analysis and long time protein dynamics. J. Phys. Chem. 100:1996;2567-2572.
9. Case, D. A. (1997). Normal mode analysis of biomolecular dynamics. In Computer Simulation of Biomolecular Systems (van Gunsteren, W. F., Weiner, P. K. & Wilkinson, A. J., eds), vol. 3, pp. 284-301, Kluwer Academic, Dordrecht.
10. Horiuchi T., Go N. Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme. Proteins: Struct. Funct. Genet. 10:1991;106-116.
11. Tasumi M., Takeuchi H., Ataka S., Dwivedi A.M., Krimm S. Normal vibrations of proteins: glucagon. Biopolymers. 21:1982;711-714.
12. Noguti T., Go N. Collective variable description of small-amplitude conformational fluctuations in a globular protein. Nature. 296:1982;776-778.
13. Tirion M.M., ben-Avraham D., Lorenz M., Holmes K.C. Normal modes as refinement parameters for the F-actin model. Biophys. J. 68:1995;5-12.
14. Faure P., Micu A., Perahia D., Doucet J., Smith J.C., Benoit J.P. Correlated intramolecular motions and diffuse X-ray scattering in lysozyme. Struct. Biol. 1:1994;124-128.
15. Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter atomic analysis. Phys. Rev. Letters. 77:1996;1905-1908.
16. Bahar I., Atilgan A.R., Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:1997;173-181.
17. Doruker P., Jernigan R.L., Bahar I. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comp. Chem. 23:2002;119-227.
18. Tama F., Wriggers W., Brooks 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.
19. Wriggers W., Milligan R.A., Schulten K., McCammon J.A. Self-organizing neural networks bridge the biomolecular resolution gap. J. Mol. Biol. 284:1998;1247-1254.
20. Wriggers W., Milligan R.A., McCammon J.A. Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 125:1999;185-195.
21. Ming D., Kong Y., Lambert M.A., Huang Z., Ma J. How to describe protein motion without amino acid sequence and atomic coordinates. Proc. Natl Acad. Sci. USA. 99:2002;8620-8625.
22. Ming D., Kong Y., Wakil S.J., Brink J., Ma J. Domain movements in human fatty acid synthase by quantized elastic deformation model. Proc. Natl Acad. Sci. USA. 99:2002;7895-7899.
23. Fritzke B. Growing cell structures - a self-organizing network for unsupervised and supervised learning. Neural Networks. 7:1994;1441-1460.
24. Bookstein F.L. Morphometric Tools for Landmark Data. 1991;Cambridge University Press, Cambridge, UK.
25. Tirion M.M., ben-Avraham D. Normal mode analysis of G-actin. J. Mol. Biol. 230:1993;186-195.
26. Tama F., Sanejouand Y.-H. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14:2001;1-6.
27. Darst S.A., Opalka N., Chacón P., Polyakov A., Richter C., Zhang G., Wriggers W. Conformational flexibility of bacterial RNA polymerase. Proc. Natl Acad. Sci. USA. 99:2002;4296-4301.
28. Zhang G., Campbell E.A., Minakhin L., Richter C., Severinov K., Darst S.A. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell. 98:1999;811-824.
29. Frank J., Agrawal R.K. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature. 406:2000;318-322.
30. Zhang X., Beuron F., Freemont P.S. Machinery of protein folding and unfolding. Curr. Opin. Struct. Biol. 12:2002;231-238.
31. Cramer P., Bushnell D.A., Kornberg R.D. Structural basis of transcription: RNA polymerase II at 2.8 Angstrom resolution. Science. 292:2001;1863-1876.
32. Tama F., Gadea F.X., Marques O., Sanejouand Y.-H. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins: Struct. Funct. Genet. 41:2000;1-7.
33. Frank J., Zhu J., Penczek P., Li Y., Srivastava S., Verschoor A., et al. A model of protein synthesis based on cryo-microscopy of the E. coli ribosome. Nature. 376:1995;441-444.
34. Frank J., Verschoor A., Li Y., Zhu J., Lata R.K., Radermacher M., et al. A model of the translational apparatus based on a three-dimensional reconstruction of the Escherichia coli ribosome. Biochem. Cell Biol. 73:1995;757-765.
35. Gabashvili I.S., Agrawal R.K., Spahn C.M.T., Grassucci R.A., Svergun D.I., Frank J., Penczek P. Solution structure of the E. Coli 70 S ribosome at 11.5 Å resolution. Cell. 100:2000;537-549.
36. Llorca O., Martin-Benito J., Ritco-Vosonvici M., Grantham, J., Hynes G.M., Willison K.R., et al. Eukaryotic chaperonin CCT stabilizes actin and tubulin folding intermediates in open quasi-native conformations. EMBO J. 19:2000;5971-5979.
37. Wriggers W., Birmanns S. Using Situs for flexible and rigid-body fitting of multi-resolution single molecule data. J. Struct. Biol. 133:2001;193-202.
38. Wriggers W., Chacón P. Modeling tricks and fitting techniques for multi-resolution structures. Structure. 9:2001;779-788.
39. Humphrey W.F., Dalke A., Schulten K. VMD - visual molecular dynamics. J. Mol. Graph. 14:1996;33-38.
40. Merritt E.A., Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524.