Molecular Dynamics Simulation of Protein Folding by Essential Dynamics Sampling: Folding Landscape of Horse Heart Cytochrome c

Biophysical Journal

Volumn 85, Issue 5, 2003, Pages 2865-2871

  Daidone, Isabella ^a   Amadei, Andrea ^b   Roccatano, Danilo ^c   Di Nola, Alfredo ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b UNIVERSITY OF ROME TOR VERGATA   (Italy)

^c UNIVERSITY OF L'AQUILA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C;

ANALYTIC METHOD; ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; HEART MUSCLE CELL; HORSE; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; PROTEIN FOLDING; SAMPLING; SIMULATION; STRUCTURE ANALYSIS;

EQUUS CABALLUS;

EID: 0242353859     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74709-2     Document Type: Article

References (42)

1. Akiyama, S., S. Takahashi, K. Ishimori, and I. Morishima. 2000. Stepwise formation of α-helices during cytochrome c folding. Nat. Struct. Biol. 7:514-520.
2. Akiyama, S., S. Takahashi, T. Kimura, K. Oishimori, I. Morishima, Y. Nishikawa, and T. Fujisawa. 2002. Conformational landscape of cytochrome c folding studied by microsecond-resolved small-angle x-ray scattering. Proc. Natl. Acad. Sci. USA. 99:1329-1334.
3. Alm, E., and D. Baker. 1999. Matching theory and experiment in protein folding. Curr. Opin. Struct. Biol. 9:189-196.
4. Alonso, D., and V. Daggett. 2000. Staphylococcal protein-a: unfolding pathways, unfolded states, and differences between the b and e domains. Proc. Natl. Acad. Sci. USA. 97:133-138.
5. Amadei, A., A. B. M. Linssen, and H. J. C. Berendsen. 1993. Essential dynamics of proteins. Prot. Struct. Funct. Genet. 17:412-425.
6. Amadei, A., A. B. M. Linssen, B. L. de Groot, D. M. van Aalten, and H. J. C. Berendsen. 1996. An efficient method for sampling the essential subspace of proteins. J. Biomol. Struct. Dyn. 13:615-625.
7. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. 1981. Interaction models for water in relation to protein hydration. In Intermolecular Forces. B. Pullman, editor. D. Reidel Publishing Company, Dordrecht, The Netherlands. 331-342.
8. Boczko, E., and C. L. Brooks, III. 1995. First-principle calculation of the folding free energy of a three-helix bundle protein. Science. 269: 393-396.
9. Brooks III, C. L. 2002. Viewing protein folding from many perspectives. Proc. Natl. Acad. Sci. USA. 99:1099-1100.
10. Brown, D., and J. H. R. Clarke. 1984. A comparison of constant energy, constant temperature, and constant pressure ensembles in molecular dynamics simulations of atomic liquids. Mol. Phys. 51:1243-1252.
11. Bushnell, G. W., G. V. Louie, and G. D. Brayer. 1990. High-resolution three-dimensional structure of horse heart cytochrome c. J. Mol. Biol. 214:585-595.
12. Colon, W., G. A. Elove, L. P. Wakem, F. Sherman, and H. Roder. 1996. Side chain packing of the N- and C-terminal helices plays a critical role in the kinetics of cytochrome c folding. Biochemistry. 35:5538-5549.
13. Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
14. de Groot, B. L., A. Amadei, D. M. F. van Aalten, and H. Berendsen. 1996. Towards an exhaustive sampling of the configurational space of the two forms of peptide hormone guanylin. J. Biomed. Str. Dyn. 13:741-751.
15. Diaz, J., B. Wroblowski, J. Schlitter, and Y. Engelborghs. 1997. Calculation of pathways for the conformational transition between the gtp- and gdp-bound states of the ha-ras-p21 protein: calculations with explicit solvent simulations and comparison with calculations in vacuum. Proteins. 28:434-451.
16. Dill, K., and H. Chan. 1997. From Levinthal to pathways to funnels. Nat. Struct. Biol. 4:10-19.
17. Dobson, C., and M. Karplus. 1999. The fundamental of protein folding: bringing together theory and experiment. Curr. Opin. Struct. Biol. 9:92-101.
18. Duan, Y., and P. Kollman. 1998. Pathways to a protein folding intermediate observed in a 1-μs simulation in aqueous solution. Science. 282: 740-744.
19. Ferrara, P., J. Apostolakis, and A. Caflisch. 2000. Computer simulations of protein folding by targeted molecular dynamics. Proteins. 39:252-260.
20. Finkelstein, A. V. 1997. Can protein unfolding simulate protein folding? Prot. Eng. 10:843-845.
21. García, A. 1992. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 66:2696-2699.
22. Guo, Z., C. L. Brooks III, and E. Boczko. 1997. Exploring the folding free energy surface of a three-helix bundle protein. Proc. Natl. Acad. Sci. USA. 94:10161-10166.
23. Hagen, S., and W. Eaton. 2000. Two-state expansion and collapse of a polypeptide. J. Mol. Biol. 301:1019-1027.
24. Lyubovitski, J., H. Gray, and J. Winkler. 2002. Mapping the cytochrome c folding landscape. J. Am. Chem. Soc. 124:5481-5485.
25. Ma, J., and M. Karplus. 1997. Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21. Proc. Natl. Acad. Sci. USA. 94:11905-11910.
26. Marmorino, J. L., M. Lehti, and G. J. Pielak. 1998. Native tertiary structure in an A-state. J. Mol. Biol. 275:379-388.
27. Mayor, U., C. M. Johnson, V. Daggett, and A. R. Fersht. 2000. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc. Natl. Acad. Sci. USA. 97:13518-13522.
28. Ohgushi, M., and A. Wada. 1983. "Molten-globule state": a compact form of globular proteins with mobile side-chains. FEBS Lett. 164:21-24.
29. Onuchic, J., Z. Luthey-Schulten, and P. Wolynes. 1997. Theory of protein folding: the energy landscape perspective. Annu. Rev. Phys. Chem. 48:545-600.
30. Pan, Y., and V. Daggett. 2001. Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: free energy perturbation calculations using transition and denaturated states from molecular dynamics of unfolding. Biochemistry. 40:2723-2731.
31. Pollack, L., M. W. Tate, N. C. Darnton, J. B. Knight, S. M. Gruner, W. A. Eaton, and R. H. Austin. 1999. Compactness of the denatured state of a fast-folding protein measured by submillisecond small-angle x-ray scattering. Proc. Natl. Acad. Sci. USA. 96:10115-10117.
32. Roccatano, D., I. Daidone, M.-A. Ceroso, C. Bossa, and A. D. Nola. 2003. Selective excitation of native fluctuations during thermal unfolding simulations: horse heart cytochrome c as a case study. Biophys. J. 84:1876-1883.
33. Ryckaert, J., and A. Bellemans. 1975. Molecular dynamics of liquid n-butane near its boiling point. Chem. Phys. Lett. 30:123-125.
34. Schlitter, J., M. Engels, P. Kruger, E. Jacoby, and A. Wollmer. 1993. Targeted molecular dynamics simulation of conformational changes: application to the t↔r transition in insulin. Mol. Sim. 10:291-309.
35. Segel, D., D. Eliezer, V. Uversky, A. Fink, K. Hodgson, and S. Doniach. 1999. Protein denaturation: a small-angle x-ray scattering study of the ensemble of unfolded states of cytochrome c. Biochemistry. 38:15352-15359.
36. Shastry, M., S. Luck, and H. Roder. 1998. A continuous-flow capillary mixing method to monitor reactions on the microsecond timescale. Biophys. J. 74:2714-2721.
37. Shea, J.-E., and C. L. Brooks, 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.
38. Sheinermann, F., and C. Brooks, III. 1998. Calculation on folding of segment vb1 of streptococcal protein-G. J. Mol. Biol. 278:439-456.
39. van Buuren, A. R., S. J. Marrink, and H. J. C. Berendsen. 1993, A molecular dynamics study of decane/water interface. J. Phys. Chem. 97:9206-9212.
40. van Gunsteren, W. F., and H. J. C. Berendsen. 1987. GROMOS Manual. BIOMOS, Biomolecular Software, Laboratory of Physical Chemistry, University of Groningen, The Netherlands.
41. van Gunsteren, W. F., S. Billeter, A. Eising, P. Hunenberger, P. Kruger, A. E. Mark, W. Scott, and I. Tironi. 1996. Biomolecular Simulations: The GROMOS96 Manual and User Guide. BIOMOS b.v., Zurich, Groningen.
42. Xu, Y., L. Mayne, and S. Englander. 1998. Evidence for an unfolding and refolding pathway in cytochrome c. Nat. Struct. Biol. 5:774-778.