Characterizing global substates of myoglobin

Structure

Volumn 6, Issue 5, 1998, Pages 587-594

  Andrews, B Kim ^a,c   Romo, Tod ^b   Clarage, James B ^b   Pettitt, B Montgomery ^a   Phillips Jr , George N ^b  

^a University of Houston   (United States)

^b RICE UNIVERSITY   (United States)

^c UNIVERSITY OF HOUSTON   (United States)

Author keywords

Conformational substates; Molecular dynamics; Myoglobin; Phase space

Indexed keywords

HUMULUS LUPULUS;

EID: 0032524416     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(98)00060-4     Document Type: Article

References (35)

1. Karplus, M. & McCammon, J.A. (1983). Dynamics of proteins: elements and function. Annu. Rev. Biochem. 53, 263-300.
2. Caspar, D.L.D., Clarage, J.B., Salunke, D.M. & Clarage, M. (1988). Liquid-like movements in crystalline insulin. Nature 332, 659-662.
3. Smith, P.E. & Pettitt, B.M. (1994) Modeling solvent in biomolecular systems. J. Phys. Chem. 98, 9700-9711.
4. Frauenfelder, H., Sligar, S.G. & Wolynes, P.G. (1991). The energy landscapes and motions of proteins. Science 254, 1598-1603.
5. Clarage, J.B. & Phillips, G.N., Jr (1994). Cross-validation tests of time-averaged molecular dynamics refinements for determination of protein structures by X-ray crystallography. Acta Crystallogr. D 50, 24-36.
6. Pearson, K. (1901). On lines and planes of closest fit to systems of points in space. Phil. Mag., Ser. 62, 559-572.
7. Schilderinck, J.H.F. (1970). Factor Analysis Applied to Developed and Developing Countries. Rotterdam University Press, Groningen, The Netherlands.
8. Kendal, M. & Stuart, A. (1966). In The Advanced Theory of Statistics Vol. 3, Ch. 43, Hafner, New York.
9. Garcia, A.E. (1992). Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68, 2696-2699.
10. de Groot, B.L., van Aalten, M.F., Amadel, A. & Berendsen, H.J.C. (1996). The consistency of large concerted motions in proteins in molecular dynamics simulations. Biophys. J. 71, 1707-1713.
11. Case, D.A. (1994). Normal mode analysis of protein dynamics. Curr. Opin. Struct. Biol. 4, 285-290.
12. Baisera, J.A., Wriggers, W., Oono, Y. & Schulten, K. (1996). Principal component analysis and long time protein dynamics. J. Phys. Chem. 100, 2567-2572.
13. Born, M. & Huang, K. (1954). Dynamical Theory of Crystal Lattices. Clarendon Press, Oxford.
14. Amadei, A., Linssen, A.B.M. & Berendsen, H.J.C. (1993). Essential dynamics of proteins. Proteins 17, 412-425.
15. Hayward, S. & Go, N. (1995). Collective variable description of native protein dynamics. Annu. Rev. Phys. Chem. 46 223-250.
16. Brooks, C.L. III, Karplus, M. & Pettitt, B.M. (1988). Proteins: a theoretical perspective of dynamics, structure, and thermodynamics. In Advances in Chemical Physics. Vol. 71. (Prigogine, I. & Rice, S., eds), John Wiley & Sons, New York.
17. Stewart, G.W. (1993). On the early history of the singular value decomposition. SIAM Review 35, 551-566.
18. Romo, T.D., Clarage, J.B., Sorensen, D.C. & Phillips, G.N., Jr (1995). Automatic identification of discrete substates in proteins: singular value decomposition analysis of time-averaged crystallographic refinements. Proteins 22, 311-321.
19. Elber, R. & Karplus, M. (1987). Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science 235, 318-321.
20. Findsen, L.A., Subramanian, S., Lounnas, V., & Pettitt, B.M. (1991). Time scales and fluctuations of protein dynamics: metmyoglobin. In Aqueous Solution in Principles of Molecular Recognition. (Buckingham, A.D., ed.), Chapman & Hall, London.
21. Steinbach, P.J. & Brooks, B.R. (1995). Protein hydration elucidated by molecular dynamics simulation. Proc. Natl Acad. Sci. USA 90, 9135-9139.
22. Phillips, G.N., Jr. & Pettitt, B.M. (1995). Structure and dynamics of the water around myoglobin. Protein Sci. 4, 149-158.
23. Hagen, S.J., Hofrichter, J. & Eaton, W.A. (1995). Protein reaction kinetics in a room-temperature glass. Science 269, 959-962.
24. Zhou, H. & Wang, L. (1996). Chaos in biomolecular dynamics. J. Phys. Chem. 100, 8101-8105.
25. Braxenthaler, M., Unger, R., Auerbach, D., Given, J.A. & Moult, J. (1997). Chaos in protein dynamics. Proteins 29, 417-425.
26. Moon, F.C. (1992). In Chaotic and Fractal Dynamics. Ch. 1, pp. 1-46, John Wiley and Sons, Inc., New York.
27. Smith, P.E., Pettitt, B.M. & Karplus, M. (1993). Stochastic dynamics simulations of the alanine depeptide using a solvent-modified potential energy surface. J. Phys. Chem. 97, 6907-6913.
28. Straub, J.E. & Thirumalai, D. (1993). Exploring the energy landscape in proteins. Proc. Natl Acad. Sci. USA 90, 809-813.
29. Clarage, J.B., Romo, T.D., Andrews, B.K., Pettitt, B.M. & Phillips, G.N., Jr. (1995). A sampling problem in molecular dynamics simulations of macromolecules. Proc. Natl Acad. Sci. USA 92, 3288-3292.
30. Mazor, M. & Pettitt, B.M. (1991). Convergence of the chemical potential in aqueous solutions. Mol. Simul. 6, 1-4.
31. Huang, X. & Boxer, S.G. (1994). Discovery of new ligand binding pathways in myoglobin by random mutagenesis. Struct. Biol. 1, 226-229.
32. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. & Karplus, M. (1983). CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4, 187.
33. Gordon, H.L. & Somorjai, R.L. (1992). Fuzzy cluster analysis of molecular dynamics trajectories. Protiens 14, 249-264.
34. MATLAB Software Package, Version 5.1. (1997). The MathWorks Inc.
35. Yager, R. & Filev, D. (1994). Generation of fuzzy rules by mountain clustering. Journal of Intelligent & Fuzzy Systems. 2, 209-219.