Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: Myosin versus kinesin

Biophysical Journal

Volumn 89, Issue 1, 2005, Pages 167-178

  Zheng, Wenjun ^a   Brooks, Bernard R ^a  

^a NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

KINESIN; MYOSIN; NUCLEOTIDE BINDING PROTEIN;

ANALYTIC METHOD; ARTICLE; COMPARATIVE STUDY; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ELASTICITY; MOLECULAR DYNAMICS; MOLECULAR PROBE; PROTEIN CONFORMATION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

EID: 23244442698     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.063305     Document Type: Article

References (29)

1. Kull, F. J., and S. A. Endow. 2002. Kinesin: switch I & II and the motor mechanism. J. Cell Sci. 115:15-23.
2. Geeves, M. A., and K. C. Holmes. 1999. Structural mechanism of muscle contraction. Annu. Rev. Biochem. 68:687-728.
3. Houdusse, A., and H. Sweeney. 2001. Myosin motors: missing structures and hidden springs. Curr. Opin. Struct. Biol. 11:182-194.
4. Kull, F. J., E. P. Sablin, R. Lau, R. J. Fletterick, and R. D. Vale. 1996. Crystal structure of the kinesin motor domain reveals a structural similarity to myosin. Nature. 380:550-555.
5. Houdusse, A., A. G. Szent-Gyorgyi, and C. Cohen. 2000. Three conformational states of scallop myosin S1. Proc. Natl. Acad. Sci. USA. 97:11238-11243.
6. Coureux, P. D., A. L. Wells, J. Menetrey, C. M. Yengo, C. A. Morris, H. L. Sweeney, and A. Houdusse. 2003. A structural state of the myosin V motor without bound nucleotide. Nature. 425:419-423.
7. Reubold, T. F., S. Eschenburg, A. Becker, F. J. Kull, and D. J. Manstein. 2003. A structural model for actin-induced nucleotide release in myosin. Nat. Struct. Biol. 10:826-830.
8. Holmes, K. C., I. Angert, F. J. Kull, W. Jahn, and R. R. Schroder. 2003. Electron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide. Nature. 425:423-427.
9. Volkmann, N., D. Hanein, G. Ouyang, K. M. Trybus, D. J. DeRosier, and S. Lowey. 2000. Evidence for cleft closure in actomyosin upon ADP release. Nat. Struct. Biol. 7:1147-1155.
10. Sack, S., F. J. Kull, and E. Mandelkow. 1999. Motor proteins of the kinesin family. Structures, variations, and nucleotide binding sites. Eur. J. Biochem. 262:1-11.
11. Yun, M., X. Zhang, C. G. Park, H. W. Park, and S. A. Endow. 2001. A structural pathway for activation of the kinesin motor ATPase. EMBO J. 20:2611-2618.
12. Wriggers, W., and K. Schulten. 1998. Nucleotide-dependent movements of the kinesin motor domain predicted by simulated annealing. Biophys. J. 75:646-661.
13. Minehardt, T. J., R. Cooke, E. Pate, and P. A. Kollman. 2001. Molecular dynamics study of the energetic, mechanistic, and structural implications of a closed phosphate tube in NCD. Biophys. J. 80:1151 -1168.
14. Vale, R. D., and R. A. Milligan. 2000. The way things move: looking under the hood of molecular motor proteins. Science. 288:88-95.
15. 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.
16. Delarue, M., and Y. H. Sanejouand. 2002. Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. J. Mol. Biol. 320:1011-1024.
17. Tama, F., and Y. H. Sanejouand. 2001. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14:1-6.
18. Zheng, W., and S. Doniach. 2003. A comparative study of motor-protein motions by using a simple elastic-network model. Proc. Natl. Acad. Sci. USA. 100:13253-13258.
19. 2+-ATPase. Biophys. J. 86:743-763.
20. Navizet, I., R. Lavery, and R. L. Jernigan. 2004. Myosin flexibility: structural domains and collective vibrations. Proteins. 54:384-393.
21. Zheng, W., and B. R. Brooks. 2005. Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model. J. Mol. Biol. 346:745-759.
22. Tirion, M. M. 1996. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1905-1908.
23. Hinsen, K. 1998. Analysis of domain motions in large proteins. Proteins. 33:417-429.
24. Brooks, B. R., D. Janezic, and M. Karplus. 1995. Harmonic analysis of large systems. J. Comput. Chem. 16:1522-1542.
25. Levy, R., A. Srinivasan, W. Olson, and J. McCammon. 1984. Quasiharmonic method for studying very low frequency modes in proteins. Biopolymers. 23:1099-1112.
26. Hayward, S., and H. J. Berendsen. 1998. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins. 30:144-154.
27. Naber, N., T. J. Minehardt, S. Rice, X. Chen, J. Grammer, M. Matuska, R. D. Vale, P. A. Kollman, R. Car, R. G. Yount, R. Cooke, and E. Pate. 2003. Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules. Science. 300:798-801.
28. Song, Y. H., A. Marx, J. Muller, G. Woehlke, M. Schliwa, A. Krebs, A. Hoenger, and E. Mandelkow. 2001. Structure of a fast kinesin: implications for ATPase mechanism and interactions with microtubules. EMBO J. 20:6213-6225.
29. Kikkawa, M., E. P. Sablin, Y. Okada, H. Yajima, R. J. Fletterick, and N. Hirokawa. 2001. Switch-based mechanism of kinesin motors. Nature. 411:439-445.