Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

Journal of Molecular Biology

Volumn 323, Issue 5, 2002, Pages 927-937

  Zagrovic, Bojan ^a   Snow, Christopher D ^a   Shirts, Michael R ^a   Pande, Vijay S ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Distributed computing; Ensemble averaging; Molecular dynamics; Protein folding; Villin headpiece

Indexed keywords

PHENYLALANINE; VILLIN;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; ATOM; CALCULATION; CARBOXY TERMINAL SEQUENCE; COMPUTER SIMULATION; HYDROPHOBICITY; MOLECULAR DYNAMICS; MOLECULAR SIZE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; THEORY;

MUS;

EID: 0036428782     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00997-X     Document Type: Article

References (40)

1. Dobson, C. M., Sali, A. & Karplus, M. (1998). Protein folding: A perspective from theory and experiment. Angew. Chem. Int. Ed. Engl. 37, 868-893.
2. Dill, K. A. & Chan, H. S. (1997). From Levinthal to pathways to funnels. Nature Struct. Biol. 4, 10-19.
3. Brooks, C. L., III, Gruebele, M., Onuchic, J. N. & Wolynes, P. G. (1998). Chemical physics of protein folding. Proc. Natl Acad. Sci. USA, 95, 11037-11038.
4. Prusiner, S. B. (1998). Prions. Proc. Natl Acad. Sci. USA, 95, 13363-13383.
5. Nelson, J. C., Saven, J. G., Moore, J. S. & Wolynes, P. G. (1997). Solvophobically driven folding of non-biological oligomers. Science, 277, 1793-1796.
6. Duan, Y. & Kollman, P. A. (1998). Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science, 282, 740-744.
7. Shea, J. E. & Brooks, C. L., III (2001). From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem. 52, 499-535.
8. Tobias, D. J. & Brooks, C. L., III (1987). Calculation of free-energy surfaces using the methods of thermodynamic perturbation-theory. Chem. Phys. Letters, 142, 472-476.
9. Bond, C. J., Wong, K. B., Clarke, J., Fersht, A. R. & Daggett, V. (1997). Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: Description of the folding pathway. Proc. Natl Acad. Sci. USA, 94, 13409-13413.
10. Fersht, A. R. & Daggett, V. (2002). Protein folding and unfolding at atomic resolution. Cell, 108, 573-582.
11. Mayor, U., Johnson, C. M., Daggett, V. & Fersht, A. R. (2000). Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc. Natl Acad. Sci. USA, 97, 13518-13522.
12. Wong, K. B., Clarke, J., Bond, C. J., Neira, J. L., Freund, S. M., Fersht, A. R. & Daggett, V. (2000). Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding. J. Mol. Biol. 296, 1257-1282.
13. Kazmirski, S. L., Wong, K. B., Freund, S. M., Tan, Y. J., Fersht, A. R. & Daggett, V. (2001). Protein folding from a highly disordered denatured state: The folding pathway of chymotrypsin inhibitor 2 at atomic resolution. Proc. Natl Acad. Sci. USA, 98, 4349-4354.
14. Shirts, M. R. & Pande, V. S. (2001). Screensavers of the world, unite!. Science, 290, 1903-1904.
15. Shirts, M. R. & Pande, V. S. (2001). Mathematical analysis of coupled parallel simulations. Phys. Rev. Letters, 86, 4983-4987.
16. Zagrovic, B., Sorin, E. J. & Pande, V. (2001). Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313, 151-169.
17. Zagrovic, B., Snow, C. D., Khaliq, S., Shirts, M. & Pande, V. S. (2002). Native-like mean Structure in the unfolded ensemble of small proteins. J. Mol. Biol. 323, 153-164.
18. McKnight, C. J., Matsudaira, P. T. & Kim, P. S. (1997). NMR structure of the 35-residue villin headpiece subdomain. Nature Struct. Biol. 4, 180-184.
19. Hardin, C., Luthey-Schulten, Z. & Wolynes, P. G. (1999). Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides. Proteins: Struct. Funct. Genet. 34, 281-294.
20. Ptitsyn, O. B. (1995). Molten globule and protein folding. Advan. Protein Chem. 47, 83-229.
21. Fersht, A. R. (1999). Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Freeman, New York.
22. Pande, V. S., Baker, I., Chapman, J., Elmer, S., Khaliq, S., Larson, S. et al. (2002). Atomistic protein folding simulations on the hundreds of microsecond time-scale using worldwide distributed computing. Biopolymers. In press.
23. Klein-Seetharaman, J., Oikawa, M., Grimshaw, S. B., Wirmer, J., Duchardt, E., Ueda, T. et al. (2002). Long-range interactions within a nonnative protein. Science, 295, 1719-1722.
24. Plotkin, S. S. (2001). Speeding protein folding beyond the Go model: How a little frustration sometimes helps. Proteins: Struct. Funct. Genet. 45, 337-345.
25. Qiu, D., Shenkin, P. S., Hollinger, F. P. & Still, W. C. (1997). The gb/sa continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J. Phys. Chem. 101, 3005-3014.
26. Shortle, D. & Ackerman, M. S. (2001). Persistence of native-like topology in a denatured protein in 8 M urea. Science, 293, 487-489.
27. Srinivasan, R. & Rose, G. D. (1999). A physical basis for protein secondary structure. Proc. Natl Acad. Sci. USA, 96, 14258-14263.
28. van Gunsteren, W. F., Brunne, R. M., Gros, P., van Schaik, R. C., Schiffer, C. A. & Torda, A. E. (1994). Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data. Methods Enzymol. 239, 619-654.
29. Gros, P., van Gunsteren, W. F. & Hol, W. G. (1990). Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics. Science, 249, 1149-1152.
30. Torda, A. E., Brunne, R. M., Huber, T., Kessler, H. & van Gunsteren, W. F. (1993). Structure refinement using time-averaged J-coupling constant restraints. J. Biomol. NMR, 3, 55-66.
31. Daura, X., Antes, I., van Gunsteren, W. F., Thiel, W. & Mark, A. E. (1999). The effect of motional averaging on the calculation of NMR-derived structural properties. Proteins: Struct. Funct. Genet. 36, 542-555.
32. Burgi, R., Pitera, J. & van Gunsteren, W. F. (2001). Assessing the effect of conformational averaging on the measured values of observables. J. Biomol. NMR, 19, 305-320.
33. Gillespie, J. R. & Shortle, D. (1997). Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures. J. Mol. Biol. 268, 170-184.
34. Gillespie, J. R. & Shortle, D. (1997). Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels. J. Mol. Biol. 268, 158-169.
35. Zhang, O., Kay, L. E., Shortle, D. & Forman-Kay, J. D. (1997). Comprehensive NOE characterization of a partially folded large fragment of staphylococcal nuclease delta131delta, using NMR methods with improved resolution. J. Mol. Biol. 272, 9-20.
36. Shortle, D., Simons, K. T. & Baker, D. (1998). Clustering of low-energy conformations near the native structures of small proteins. Proc. Natl Acad. Sci. USA, 95, 11158-11162.
37. Onuchic, J. N. (1997). Contacting the protein folding funnel with NMR. Proc. Natl Acad. Sci. USA, 94, 7129-7131.
38. Andersen, H. C. (1983). Rattle: A "velocity" version of the shake algorithm for molecular dynamics calculations. J. Comput. Phys. 52, 24-34.
39. Jorgensen, W. L. & Tirado-Rives, J. (1988). The OPLS potential functions for proteins: Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110, 1666-1671.
40. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.