Refolding molecular dynamics simulations of small- and middle-sized proteins in an explicit solvent

Molecular Simulation

Volumn 28, Issue 4, 2002, Pages 337-357

  Suenaga, Atsushi ^a,b   Okimoto, Noriaki ^a   Ebisuzaki, Toshikazu ^a  

^a INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

helix; sheet; Molecular dynamics; Protein folding; Tertiary structure

Indexed keywords

COMPUTER SIMULATION; HYDROGEN BONDS; MOLECULAR DYNAMICS; PROBLEM SOLVING; SOLVENTS;

Α-HELIX; Β-SHEET; PROTEIN FOLDING; TERTIARY STRUCTURE;

PROTEINS;

EID: 0042966056     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020290018732     Document Type: Article

References (42)

1. Yankner, B.A., Dawes, L.R., Fisher, S., Villa-Komaroff, L., Oster-Granite, M.L. and Neve, R.L. (1989) "Neurotoxicity of a fragment of the amyloid precursor associated with Alzheimer's disease", Science 245, 417.
2. Prusiner, S.B. (1997) "Prion diseases and the BSE crisis", Science 278, 245.
3. Hagen, S.J., Hofrichter, J., Szabo, A. and Eaton, W.A. (1996) "Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding", Proc. Natl Acad. Sci. USA 93, 11615.
4. Burton, R.E., Huang, G.S., Daugherty, M.A., Calderone, T.L. and Oas, T.G. (1997) "The energy landscape of a fast-folding protein mapped by Ala → Gly substitutions", Nat. Struct. Biol. 4, 305.
5. Tobias, D.J., Mertz, J.E. and Brooks III, L. (1991) "Nanosecond time scale folding dynamics of a pentapeptide in water", Biochemistry 30, 6054.
6. Sung, S.-S. and Wu, X.-W. (1996) "Molecular dynamics simulations of synthetic peptide folding", Proteins 25, 202.
7. Demchuk, E., Bashford, D. and Case, D A. (1997) "Dynamics of a type VI reverse turn in a linear peptide in aqueous solution", Fold Des. 2, 35.
8. Prevost, M. and Ortmans, I. (1997) "Refolding simulations of an isolated fragment of barnase into a native-like β hairpin: evidence for compactness and hydrogen bonding as concurrent stabilizing factors", Proteins 29, 212.
9. Daura, X., Jaun, B., Seebach, D. and van Gunsteren, W.F. (1998) "Reversible peptide folding in solution by molecular dynamics simulation", J. Mol. Biol. 280, 925.
10. Chipot, C., Maigret, B. and A., Pohorille (1999) "Early events in the folding of an amphipathic peptide: a multinanosecond molecular dynamics study", Proteins 36, 383.
11. Wang, H., Varady, J., Ng, L. and Sung, S.-S. (1999) "Molecular dynamics simulations of β-hairpin folding", Proteins 37, 325.
12. Bonvin, A.M.J.J. and van Gunsteren, W.F. (2000) "β-hairpin stability and folding: molecular dynamics studies of the first β-hairpin of Tendamistat", J. Mol. Biol. 296, 255.
13. Duan, Y. and Kollman, P.A. (1998) "Pathway to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution", Science 282, 740.
14. Skolnick, J. and Kolinski, A. (1990) "Simulations of the folding of a globular protein", Science 250, 1121.
15. Šali, A., Shakhnovich, E. and Karplus, M. (1994) "How does a protein fold?", Nature 369, 248.
16. Dill, K.A., Bromberg, S., Yue, K., Fiebig, K.M., Yee, D.P., Thomas, P.D. and Chan, H.S. (1995) "Principles of protein folding-a perspective from simple exact models", Protein Sci. 4, 561.
17. Lazaridis, T. and Karplus, M. (1997) "New view of protein folding reconciled with the old through multiple unfolding simulations", Science 278, 1928.
18. Kim, P.S. and Baldwin, R.L. (1982) "Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding", Annu. Rev. Biochem. 51, 459.
19. Dill, K.A. (1985) "Theory for the folding and stability of globular proteins", Biochemistry 24, 1501.
20. Baldwin, R.L. and Rose, G.D. (1999) "Is protein folding hierarchic? I. Local structure and peptide folding", Trends Biochem. Sci. 24, 26.
21. Baldwin, R.L. and Rose, G.D. (1999) "Is protein folding hierarchic?II. Folding intermediates and transition states", Trends Biochem. Sci. 24, 77.
22. Itzhaki, L.S., Otzen, D.E. and Fersht, A.R. (1995) "The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods", J. Mol. Biol. 254, 260.
23. Jia, Z., Vandonselaar, M., Hengstenberg, W., Quail, J.W. and Delbaere, L.T.J. (1994) "The 1.6 Å structure of histidine-containing phosphotransfer protein HPr from Streptococcus faecalis", J. Mol. Biol. 236, 1341.
24. Dahiyat, B.I., Sarisky, C.A. and Mayo, S.L. (1997) "De novo protein design: towards fully automated sequence selection", J. Mol. Biol. 273, 789.
25. Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham, III, T.E., Rose, III, W.S., Simmerling, III, C.L., Darden, III, T.A., Merz, III, K.M. and Stanton, III, R.V. (1997) AMBER 5.0 (University of California, San Francisco).
26. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W. and Klein, M.L. (1983) "Comparison of simple potential functions for simulating liquid water", J. Chem. Phys 79, 926.
27. Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. and Kollman, P.A. (1995) "A second generation force field for the simulation of proteins and nucleic acids", J. Am. Chem. Soc. 117, 5179.
28. Berendsen, H.J.C., Postma, J.M.P., van Gunsteren, W.F., DiNola, A. and Haak, J.R. (1984) "Molecular dynamics with coupling to an external bath", J. Comp. Phys 81, 3684.
29. Ryckaert, J.-P., Ciccotti, G. and Berendsen, J.C. (1977) "Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes", J. Comp. Phys 23, 327.
30. Laskowski, R.A., MacArthur, M.W. and Thornton, J.M. (1993) "PROCHECK: a program to check the stereochemical quality of protein structures", J. Appl. Crystallog. 26, 283.
31. Koradi, R., Billeter, M. and Wüthrich, K. (1996) "MOLMOL: a program for display and analysis of macromolecular structures", J. Mol. Graph. 14, 51.
32. Suenaga, A., Komeiji, Y., Uebayasi, M., Meguro, T. and Yamato, I. (1998) "Molecular dynamics simulation of unfolding of histidine-containing phosphocarrier protein in water", J. Chem. Software 4, 127.
33. Sundaralingam, M. and Selharadu, Y.C. (1989) "Water-inserted α-helical segments implicate reverse turns as folding intermediates", Science 244, 1333.
34. Muck, S.M., Martinez, G.V., Fiori, W.R., Todd, A.P. and Millhauser, G.L. (1992) "Short alanine-based peptides may form 3(10)-helices and not alpha-helices in aqueous solution", Nature 359, 653.
35. Williams, S., Causgrove, T.P., Gilmanshin, R., Fang, K.S., Callender, R.H., Woodruff, W.H. and Dyer, R.B. (1996) "Fast events in protein folding: helix melting and formation in a small peptide", Biochemistry 35, 691.
36. Thompson, P.A., Eaton, W.A. and Holfrichter, J. (1997) "Laser temperature jump study of the helix ⇔ coil kinetics of an alanine peptide interpreted with a "kinetic zipper" model", Biochemistry 36, 9200.
37. Ando, T. (2000) Personal communication, Science University of Tokyo.
38. Van Nuland, N.A.J., Meijberg, W., Warner, J., Forge, V., Scheck, R.M., Robillard, G.T. and Dobson, C.M. (1998) "Slow cooperative folding of a small globular protein HPr", Biochemistry 37, 622.
39. Munoz, V., Thompson, P.A., Hofrichter, J. and Eaton, W.A. (1997) "Folding dynamics and mechanism of β-hairpin formation", Nature 390, 196.
40. Otzen, D.E., Itzhaki, L.S., Elmasry, N.F., Jackson, S.E. and Fersht, A.R. (1994) "Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding", Proc. Natl Acad. Sci. USA 91, 10422.
41. Daggett, V., Li, A., Itzhaki, L.S., Otzen, D.E. and Fersht, A.R. (1996) "Structure of the transition state for folding of a protein derived from experiment and simulation", J. Mol. Biol. 257, 430.
42. Narumi, T., Susukita, R., Ebisuzaki, T., McNiven, G. and Elmegreen, B. (1999) "Molecular dynamics machine: special-purpose computer for molecular dynamics simulations", Mol. Simul. 21, 401.