Applications of normal mode analysis in structural refinement of supramolecular complexes

Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems

Volumn , Issue , 2005, Pages 137-154

  Ma, Jianpeng ^a  

^a RICE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 47249108056     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (66)

1. Brooks III, C.L., Karplus, M., and Pettitt, B.M., Proteins: A theoretical perspective of dynamics, structure, and thermodynamics, Adv. Chem. Phys.,71,1 (1988).
2. McCammon, J.A. and Harvey, S., Dynamics of Proteins and Nucleic Acids, Cambridge University Press, Cambridge (1987).
3. Brooks, B.R., Janezic, D., and Karplus, M., Harmonic analysis of large systems. I. Methodology, J. Comput. Chem.,16, 1522 (1995).
4. Janezic, D., Venable, R.M., and Brooks, B.R., Harmonic analysis of large systems. III. Comparison with molecular dynamics, J. Comput. Chem.,16,1554 (1995).
5. Amadei, A., Linssen, A.B.M., and Berendsen, H.J.C., Essential dynamics of proteins, Proteins,17, 412 (1993).
6. Ma, J. and Karplus, M., Ligand-induced conformational changes in ras p21: A normal mode and energy minimization analysis, J. Mol. Biol.,274, 114 (1997).
7. Ma, J. and Karplus, M., The allosteric mechanism of the chaperonin GroEL: A dynamic analysis, Proc. Natl Acad. Sci. USA,95, 8502 (1998).
8. Brooks, B. and Karplus, M., Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme, Proc. Natl Acad. Sci. USA,82,4995 (1985).
9. Levitt, M., Sander, C., and Stern, P.S., Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme, J. Mol. Biol.,181, 423 (1985).
10. Seno, Y. and Go, N., Deoxymyoglobin studied by the conformational normal mode analysis II. The conformational change upon oxygenation, J. Mol. Biol., 216, 111 (1990).
11. Seno, Y. and Go, N., Deoxymyoglobin studied by the conformational normal mode analysis. I. Dynamics of globin and the heme-globin interaction, J. Mol. Biol.,216, 95 (1990).
12. Thomas, A., Field, M.J., and Perahia, D., Analysis of the low-frequency normal modes of the R state of aspartate transcarbamylase and a comparison with the T state modes, J. Mol. Biol., 261, 490 (1996).
13. Thomas, A., Field, M.J., Mouawad, L., and Perahia, D., Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase, J. Mol. Biol., 257, 1070 (1996).
14. Thomas, A., Hinsen, K., Field, M.J., and Perahia, D., Tertiary and quaternary conformational changes in aspartate transcarbamylase: A normal mode study, Proteins,34, 96 (1999).
15. Li, G. and Cui, Q., A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to Ca(2+)-ATPase, Biophys. J.,83,2457(2002).
16. Cui, Q., Li, G., Ma, J., and Karplus, M., A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase, J. Mol. Biol.,340, 345 (2004).
17. Xu, C., Tobi, D., and Bahar, I., Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<->R2 transition, J. Mol. Biol.,333, 153 (2003).
18. Wang, Y., Rader, A.J., Bahar, I., and Jemigan, R.L., Global ribosome motions revealed with elastic network model, J. Struct. Biol.,147, 302 (2004).
19. Keskin, O., Bahar, I., Flatow, D., Covell, D.G., and Jernigan, R.L., Molecular mechanisms of chaperonin GroEL-GroES Function, Biochemistry,41, 491 (2002).
20. Tama, F. and Sanejouand, Y.H., Conformational change of proteins arising from normal mode calculations, Protein Eng.,14,1 (2001).
21. Tama, F. and Brooks III, C.L., The mechanism and pathway of ph induced swelling in cowpea chlorotic mottle virus, J. Mol. Biol.,318, 733 (2002).
22. Ma, J., New advances in normal mode analysis of supermolecular complexes and applications to structural refinement, Curr. Protein Pept. Sci.,5,119 (2004).
23. Bahar, I., Atilgan, A.R., and Erman, B., Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential, Fold. Des.,2,173 (1997).
24. Haliloglu, T., Bahar, I., and Erman, B., Gaussian dynamics of folded proteins, Phys. Rev. Lett,79, 3090 (1997).
25. Atilgan, A.R., Durell, S.R., Jernigan, R.L., Demirel, M.C., Keskin, O., and Bahar, I., Anisotropy of fluctuation dynamics of proteins with an elastic network model, Biophys. J.,80, 505 (2001).
26. Tirion, M.M., Large amplitude elastic motions in proteins from a single-parameter, atomic analysis, Phys. Rev. Lett.,77, 1905 (1996).
27. MacKerell, A.D., Bashford, D., Jr., Bellott, M., Dunbrack, R.L., Jr., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuch-nir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, I., W.E., Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, J., Watanabe, M., JWiorkiewicz-Kuczera, J., Yin, D., and Karplus, M., All-atom empirical potential for molecular modeling and dynamics studies of proteins, J. Phys. Chem., B102, 3586 (1998).
28. Doruker, P., Jernigan, R.L., and Bahar, I., Dynamic of large proteins through hierarchical levels of coarse-grained structures, J. Comput. Chem.,23, 119 (2002).
29. Hinsen, K., Analysis of domain motions by approximate normal mode calculations, Proteins,33, 417 (1998).
30. Tama, F., Valle, M., Frank, J., and Brooks III, C.L., Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy, Proc. Natl Acad. Sci. USA,100, 9319 (2003).
31. Kim, M.K., Jernigan, R.L., and Chirikjian, G.S., An elastic network model of HK97 capsid maturation, J. Struct. Biol.,143, 107 (2003).
32. Kundu, S., Melton, J.S., Sorensen, D.C., and Phillips, G.N., Jr., Dynamics of proteins in crystals: Comparison of experiment with simple models, Biophys. J.,83, 723 (2002).
33. Ming, D., Kong, Y., Lambert, M., Huang, Z., and Ma, J., How to describe protein motion without amino-acid sequence and atomic coordinates, Proc. Natl Acad. Sci. USA,99, 8620 (2002).
34. Tama, F., Wriggers, W., and Brooks, C.L., Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory, J. Mol. Biol.,321,297 (2002).
35. Doruker, P. and Jernigan, R.L., Functional motions can be extracted from on-lattice construction of protein structures, Proteins,53, 174 (2003).
36. Gray, R.M., Vector quantization, IEEE ASSP Mag.,1,4 (1984).
37. Martinetz, T.M., Berkovich, S.G., and Schulten, K.J., –Neural-gas— network for vector quantization and its application to time-series prediction, IEEE Trans. Neural Networks,4, 558 (1993).
38. Makhoul, J., Roucos, S., and Gish, H., Vector quantization in speech coding, Proc. IEEE,73, 1551 (1985).
39. Flynn, T.C. and Ma, J., Theoretical analysis of twist/bend ratio and mechanical moduli of bacterial flagellar hook and filament, Biophys. J.,86, 3204 (2004).
40. 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, 7895 (2002).
41. Stoops, J.K., Ross, P., Arslanian, M.J., Aune, K.C., Wakil, S.J., and Oliver, R.M., Physicochemical studies of the rat liver and adipose fatty acid synthetases, J. Biol. Chem.,254, 7418 (1979).
42. Stoops, J.K. and Wakil, S.J., Animal fatty acid synthetase. A novel arrangement of the beta-ketoacyl synthetase sites comprising domains of the two subunits, J. Biol. Chem,256, 5128 (1981).
43. Stoops, J.K., Wakil, S.J., Uberbacher, E.C., and Bunick, G.J., Small-angle neutronscattering and electron microscope studies of the chicken liver fatty acid synthase, J. Biol. Chem,262, 10246 (1987).
44. Singh, N., Wakil, S.J., and Stoops, J.K., On the question of half- or full-site reactivity of animal fatty acid synthetase, J. Biol. Chem.,259, 3605 (1984).
45. Brink, J., Ludtke, S.J., Yang, C.Y., Gu, Z.W., Wakil, S.J., and Chiu, W., Quaternary structure of human fatty acid synthase by electron cryomicroscopy, Proc. Natl Acad. Sci. USA,99, 138 (2002).
46. Brink, J., Ludtke, S.J., Kong, Y., Wakil, S.J., Ma, J., and Chiu, W., Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis, Structure (Camb.),12, 185 (2004).
47. Kong, Y., Ming, D., Wu, Y., Stoops, J.K., Zhou, Z.H., and Ma, J., Conformational flexibility of pyruvate dehydrogenase complexes: A computational analysis by quantized elastic deformational model, J. Mol. Biol.,330, 129 (2003).
48. Beuron, F., Flynn, T.C., Ma, J., Kondo, H., Zhang, X., and Freemont, P.S., Motions and negative cooperativity between p97 domains revealed by cryoelec-tron microscopy and quantized elastic deformational model, J. Mol. Biol.,327,619(2003).
49. Chacon, P., Tama, F., and Wriggers, W., Mega-dalton biomolecular motion captured from electron microscopy reconstructions, J. Mol. Biol.,326,485 (2003).
50. Carazo, J.M., Accessing information on the conformational flexibility of molecular machines, Structure,12,170 (2004).
51. Ludtke, S.J., Jakana, J., Song, J.L., Chuang, D., and Chiu, W., A 11.5 Â single particle reconstruction of GroEL using EMAN, J. Mol. Biol.,314,253 (2001).
52. Ludtke, S.J., Baldwin, P.R., and Chiu, W., EMAN: semiautomated software for high-resolution single-particle reconstructions, J. Struct. Biol.,128, 82 (1999).
53. Grigorieff, N., Resolution measurement in structures derived from single particles, Acta Crystallogr. D,56,1270 (2000).
54. Tama, F., Miyashita, O., and Brooks III, C.L., Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM, J. Struct. Biol.,147, 315 (2004).
55. Ming, D., Kong, Y., Wu, Y., and Ma, J., Substructure synthesis method for simulating large molecular complexes, Proc. Natl Acad. Sci. USA,100,104 (2003).
56. Temple, G. and Bickley, W.G., Rayleigh’s Principle and its Applications to Engineering, Dover, New York (1956).
57. Chen, H., Bernstein, B.W., and Bamburg, J.R., Regulating actin-filament dynamicsin vivo, Trends Biochem. Sci.,25,19 (2000).
58. Oda, T., Makino, K., Yamashita, I., Namba, K., and Maeda, Y., Distinct structural changes detected by x-ray fiber diffraction in stabilization of F-actin by lowering pH and increasing ionic strength, Biophys.J.,80, 841 (2001).
59. Yasuda, R., Miyata, H., and Kinosita, K., Jr., Direct measurement of the torsional rigidity of single actin filaments, J. Mol. Biol.,263, 227 (1996).
60. Ming, D., Kong, Y., Wu, Y., and Ma, J., Simulation of F-actin filaments of several microns, Biophys. J.,85,27 (2003).
61. Wu, Y. and Ma, J., Refinement of F-actin model against fibre diffraction data by long-range normal modes, Biophys.J.,86, 116 (2004).
62. Wu, Y. and Ma, J., Normal-mode-based refinement of an F-actin model against fibre diffraction data, Fibre Diff. Rev.,12, 25 (2004).
63. Stubbs, G., Development in Fibre Diffraction, Curr. Opin. Struct. Biol.,9, 615(1999).
64. Wang, H. and Stubbs, G., Molecular dynamics in refinement against fibre diffraction data, Acta Crystallogr. A,49, 504 (1993).
65. ben-Avraham, D. and Tirion, M.M., Dynamic and elastic properties of F-actin: A normal-modes analysis, Biophys. J.,68,1231 (1995).
66. Holmes, K.C., Popp, D., Gebhard, W., and Kabsch, W., Atomic model of the actin filament, Nature,347, 44 (1990).