The role of shape in determining molecular motions

Biophysical Journal

Volumn 89, Issue 4, 2005, Pages 2395-2401

  Lu, Mingyang ^a   Ma, Jianpeng ^a,b  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b Rice University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS; ANISOTROPY; ARTICLE; CHEMICAL STRUCTURE; DEFORMATIONAL MOTION; ELASTIC NORMAL MODE ANALYSIS; ELASTICITY; HESSIAN MATRIX ELEMENT; MACROMOLECULE; MATHEMATICAL PHENOMENA; MOLECULAR DYNAMICS; MOLECULAR MOTION; MOLECULAR SHAPE; RANDOMIZATION; RIGIDITY;

EID: 25844525600     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.065904     Document Type: Article

References (48)

1. Brooks III, C. L., M. Karplus, and B. M. Pettitt. 1988. Proteins: a theoretical perspective of dynamics, structure, and thermodynamics. Adv. Chem. Phys. 71:1-249.
2. McCammon, J. A., and S. Harvey. 1987. Dynamics of Proteins and Nucleic Acids. Cambridge University Press, Cambridge.
3. Brooks, B. R., D. Janezic, and M. Karplus. 1995. Harmonic analysis of large systems. I. Methodology. J. Comput. Chem. 16:1522-1542.
4. Levitt, M., C. Sander, and P. S. Stern. 1985. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 181:423-447.
5. Ma, J., and M. Karplus. 1998. The allosteric mechanism of the chaperonin GroEL: a dynamic analysis. Proc. Natl. Acad. Sci. USA. 95:8502-8507.
6. Ma, J., and M. Karplus. 1997. Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis. J. Mol. Biol. 274:114-131.
7. Seno, Y., and N. Go. 1990. Deoxymyoglobin studied by the conformational normal mode analysis. I. Dynamics of globin and the heme-globin interaction. J. Mol. Biol. 216:95-109.
8. Seno, Y., and N. Go. 1990. Deoxymyoglobin studied by the conformational normal mode analysis II. The conformational change upon oxygenation. J. Mol. Biol. 216:111-126.
9. Thomas, A., M. J. Field, and D. Perahia. 1996. 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. 261:490-506.
10. Thomas, A., M. J. Field, L. Mouawad, and D. Perahia. 1996. Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase. J. Mol. Biol. 257:1070-1087.
11. Thomas, A., K. Hinsen, M. J. Field, and D. Perahia. 1999. Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study. Proteins. 34:96-112.
12. Li, G., and Q. Cui. 2002. A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase. Biophys. J. 83:2457-2474.
13. Cui, Q., G. Li, J. Ma, and M. Karplus. 2004. A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. J. Mol. Biol. 340:345-372.
14. Krebs, W. G., V. Alexandrov, C. A. Wilson, N. Echols, H. Yu, and M. Gerstein. 2002. Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins. 48:682-695.
15. Tirion, M. M. 1996. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1905-1908.
16. Atilgan, A. R., S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar. 2001. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80:505-515.
17. Ma, J. 2004. New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. Curr. Protein Pept. Sci. 5:119-123.
18. Ming, D., Y. Kong, Y. Wu, and J. Ma. 2003. Simulation of F-actin filaments of several microns. Biophys. J. 85:27-35.
19. Ming, D., Y. Kong, S. J. Wakil, J. Brink, and J. Ma. 2002. Domain movements in human fatty acid synthase by quantized elastic deformational model. Proc. Natl. Acad. Sci. USA. 99:7895-7899.
20. Kong, Y., D. Ming, Y. Wu, J. K. Stoops, Z. H. Zhou, and J. Ma. 2003. Conformational flexibility of pyruvate dehydrogenase complexes: a computational analysis by quantized elastic deformational model. J. Mol. Biol. 330:129-135.
21. Beuron, F., T. C. Flynn, J. Ma, H. Kondo, X. Zhang, and P. S. Freemont. 2003. Motions and negative cooperativity between p97 domains revealed by cryoelectron microscopy and quantized elastic deformational model. J. Mol. Biol. 327:619-629.
22. Keskin, O., I. Bahar, D. Flatow, D. G. Covell, and R. L. Jernigan. 2002. Molecular mechanisms of chaperonin GroEL-GroES function. Biochemistry. 41:491-501.
23. Wang, Y., A. J. Rader, I. Bahar, and R. L. Jernigan. 2004. Global ribosome motions revealed with elastic network model. J. Struct. Biol. 147:302-314.
24. Xu, C., D. Tobi, and I. Bahar. 2003. Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T ↔ R2 transition. J. Mol. Biol. 333:153-168.
25. Tama, F., M. Valle, J. Frank, and C. L. Brooks III. 2003. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl. Acad. Sci. USA. 100:9319-9323.
26. Tama, F., and C. L. Brooks III. 2002. The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J. Mol. Biol. 318:733-747.
27. Chacon, P., F. Tama, and W. Wriggers. 2003. Mega-dalton biomolecular motion captured from electron microscopy reconstructions. J. Mol. Biol. 326:485-492.
28. Miyashita, O., J. N. Onuchic, and P. G. Wolynes. 2003. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc. Natl. Acad. Sci. USA. 100:12570-12575.
29. Kundu, S., J. S. Melton, D. C. Sorensen, and G. N. Phillips Jr. 2002. Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys. J. 83:723-732.
30. Brink, J., S. J. Ludtke, Y. Kong, S. J. Wakil, J. Ma, and W. Chiu. 2004. Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis. Structure (Camb). 12:185-191.
31. Carazo, J. M. 2004. Accessing information on the conformational flexibility of molecular machines. Structure. 12:170-171.
32. Tama, F., O. Miyashita, and C. L. Brooks III. 2004. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J. Struct. Biol. 147:315-326.
33. Wu, Y., and J. Ma. 2004. Normal-mode-based refinement of an F-actin model against fibre diffraction data. Fibre Diff. Rev. 12:25-28.
34. Wu, Y., and J. Ma. 2004. Refinement of F-actin model against fibre diffraction data by long-range normal modes. Biophys. J. 86:116-124.
35. MacKerell Jr., A. D., D. Bashford Jr., M. Bellott, R. L. Dunbrack Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stole, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B102:3586-3616.
36. Doruker, P., R. L. Jernigan, and I. Bahar. 2002. Dynamic of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23:119-127.
37. Doruker, P., and R. L. Jernigan. 2003. Functional motions can be extracted from on-lattice construction of protein structures. Proteins. 53:174-181.
38. Ming, D., Y. Kong, M. Lambert, Z. Huang, and J. Ma. 2002. How to describe protein motion without amino-acid sequence and atomic coordinates. Proc. Natl. Acad. Sci. USA. 99:8620-8625.
39. Tama, F., W. Wriggers, and C. L. Brooks. 2002. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J. Mol. Biol. 321:297-305.
40. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
41. Bagci, Z., A. Kloczkowski, R. L. Jernigan, and I. Bahar. 2003. The origin and extent of coarse-grained regularities in protein internal packing. Proteins. 53:56-67.
42. Van Wynsberghe, A. W., and Q. Cui. 2005. Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys. J. In press.
43. Marques, O., and Y. H. Sanejouand. 1995. Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins. 23:557-560.
44. McCammon, J. A., B. R. Gelin, M. Karplus, and P. G. Wolynes. 1976. The hinge-bending mode in lysozyme. Nature. 262:325-326.
45. Brooks, B., and M. Karplus. 1985. Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. USA. 82:4995-1999.
46. Bahar, I., A. R. Atilgan, and B. Erman. 1997. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:173-181.
47. Halle, B. 2002. Flexibility and packing in proteins. Proc. Natl. Acad. Sci. USA. 99:1274-1279.
48. Ma, J. 2005. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure. 13:373-380.