Collective protein dynamics in relation to function

Current Opinion in Structural Biology

Volumn 10, Issue 2, 2000, Pages 165-169

  Berendsen, Herman Jc ^a   Hayward, Steven ^b  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

COMPUTER SIMULATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; REVIEW;

EID: 0034127361     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(00)00061-0     Document Type: Review

References (34)

1. Kitao A., Go N. Investigating protein dynamics in collective coordinate space. Curr Opin Struct Biol. 9:1999;164-169. A broader review than this - it describes applications of collective coordinate space analyses to the nature of the conformational energy surface and refinement of experimental data. It gives a clear idea of the importance of this field and its future directions.
2. Hayward S., Go N. Collective variable description of native protein dynamics. Annu Rev Phys Chem. 46:1995;223-250.
3. Hayward S. Normal mode analysis of biological molecules. Becker O.M., MacKerell A.D. Jr., Roux B., Watanabe M. Computational Biochemistry and Biophysics. 2000;Marcel Dekker, New York. in press.
4. de Groot B.L., van Aalten D.M.F., Scheek R.M., Amadei A., Vriend G., Berensdsen H.J.C. Prediction of protein conformational freedom from distance constraints. Proteins. 29:1997;240-251.
5. Bahar I., Erman B., Haliloǧlu T., Jernighan R.L. Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations. Biochemistry. 36:1997;13512-13523.
6. Haliloǧlu T., Bahar I. Coarse-grained simulations of conformational dynamics of proteins: applications to apomyoglobin. Proteins. 31:1998;271-281.
7. Amadei A., Linssen A.B.M., Berendsen H.J.C. Essential dynamics of proteins. Proteins. 17:1993;412-425.
8. García A.E. Large amplitude nonlinear motions in proteins. Phys Rev Lett. 68:1992;2696-2699.
9. 10-/α-helix transition: implications for a natural reaction coordinate. J Am Chem Soc. 116:1994;6307-6315.
10. Balsera M.A., Wriggers W., Oono Y., Schulten K. Principal component analysis and long time protein dynamics. J Phys Chem. 100:1996;2567-2572.
11. de Groot B.L., van Aalten D.M.F., Amadei A., Berendsen H.J.C. The consistency of large concerted motions in proteins in molecular dynamics simulations. Biophys J. 71:1996;1707-1713.
12. Amadei A., de Groot B.L., Cerusa M-A., Paci M., Di Nola A., Berendsen H.J.C. A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins. 35:1999;283-292.
13. Amadei A., Cerusa M.A., Di Nola A. On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations. Proteins. 36:1999;419-424.
14. Kitao A., Hayward S., Go N. Energy landscape of a native protein: jumping-among-minima model. Proteins. 33:1998;496-517.
15. Wriggers W., Schulten K. Protein domain movements: detection of rigid domains and visualization of hinges in comparison of atomic coordinates. Proteins. 29:1997;1-14.
16. Hayward S., Berendsen H.J.C. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins. 30:1998;144-154.
17. Hinsen K., Thomas A., Field M.J. Analysis of domain motions in large proteins. Proteins. 34:1999;369-382.
18. Hayward S. Structural principles governing domain motions in proteins. Proteins. 36:1999;425-435. Proteins for which at least two experimentally determined conformations are available were analyzed in terms of dynamic domains, hinge axes and hinge-bending regions. The purpose was to determine whether any structural motifs involved in controlling interdomain motions could be identified. Individual cases often represent an experimentally determined functional motion and provide an opportunity to assess simulations by comparison.
19. de Groot B.L., Vriend G., Berendsen H.J.C. Conformational changes in the chaperonin GroEL: new insights into the allosteric mechanism. J Mol Biol. 286:1999;1241-1250. CONCOORD simulations of single-ring and double-ring structures of GroEL were made. Molecular dynamics simulations of structures of this size would not be currently feasible. The results indicate coupling between the conformational change associated with nucleotide binding and that associated with GroES binding, but only in the double-ring simulations, not in simulations of single rings.
20. Ma J., Karplus M. The allosteric mechanism of the chaperonin GroEL: a dynamic analysis. Proc Natl Acad Sci USA. 95:1998;8502-8507.
21. Mouawad L., Perahia D. Diagonalization in a mixed basis: a method to compute low-frequency normal modes for large macromolecules. Biopolymers. 33:1993;599-611.
22. Thomas A., Hinsen K., Field M.J., Perahia D. Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study. Proteins. 34:1999;96-112.
23. Miller D.W., Agard D.A. Enzyme specificity under dynamic control: a normal mode analysis of alpha-lytic protease. J Mol Biol. 286:1999;267-278. Given the level of approximation in normal mode analysis, it is surprising that the results of this study can be linked so well to experimental results. It is shown how a mutant can affect the dynamics and, thus, the function of an enzyme by influencing fluctuations in the size of the substrate-binding pocket.
24. Horstink L.M., Abseher R., Nilges M., Hilbers C.W. Functionally important correlated motions in the single-stranded DNA-binding protein encoded by filamentous phage Pf3. J Mol Biol. 287:1999;569-578.
25. Chau P-L., van Aalten D.M.F., Bywater R.P., Findlay J.B.C. Functional concerted motions in the bovine serum retinol-binding protein. J Comput Aided Mol Des. 13:1999;11-20.
26. van Aalten D.M.F., Conn D.A., de Groot B.L., Findlay J.B.C., Berendsen H.J.C., Amadei A. Protein dynamics derived from clusters of crystal structures. Biophys J. 73:1997;2891-2896.
27. de Groot B.L., Hayward S., van Aalten D.M.F., Amadei A., Berendsen H.J.C. Domain motions in bacteriophage T4 lysozyme; a comparison between molecular dynamics and crystallographic data. Proteins. 31:1998;116-127.
28. Lins R.D., Briggs J.M., Straatsma T.P., Carlson H.A., Greenwald J., Choe S., McCammon J.A. Biophysical theory and modeling - molecular dynamics studies on the HIV-1 integrase catalytic domain. Biophys J. 76:1999;2999-3011.
29. Kazmierkiewicz R., Czaplewski C., Lammek B., Ciarkowski J. Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories. J Comput Aided Mol Des. 13:1999;21-33.
30. Lu H., Schulten K. Steered molecular dynamics simulations of force-induced protein domain unfolding. Proteins. 35:1999;453-463.
31. Creveld L.D., Amadei A., van Schaik R.C., Pepermans H.A.M., de Vlieg J., Berendsen H.J.C. Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations. Proteins. 33:1998;253-264.
32. Roccatano D., Amadei A., Di Nola A., Berendsen H.J.C. A molecular dynamics study of the 41-56 β-hairpin from B1 domain of protein G. Protein Sci. 8:1999;2130-2143.
33. Kazmirski S.L., Li A., Daggett V. Analysis methods for comparison of multiple molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles. J Mol Biol. 290:1999;283-304.
34. García A.E., Hummer G. Conformational dynamics of cytochrome c: correlation to hydrogen exchange. Proteins. 36:1999;175-191. Molecular dynamics simulations of horse heart cytochrome c at different temperatures were analyzed with a view to understanding the nature of the motion within the rugged energy landscape and hydrogen exchange. Large fluctuations were found to be associated with regions that move concertedly and were not necessarily correlated with hydrogen exchange.