Conformational dynamics of cytochrome c: Correlation to hydrogen exchange

Proteins: Structure, Function and Genetics

Volumn 36, Issue 2, 1999, Pages 175-191

  García, Angel E ^a   Hummer, Gerhard ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

Hydration dynamics; Molecular dynamics; Nonlinear dynamics; Protein hydration; Strange dynamics

Indexed keywords

CYTOCHROME C;

ALPHA HELIX; AQUEOUS SOLUTION; ARTICLE; CONFORMATIONAL TRANSITION; CORRELATION FUNCTION; ENZYME CONFORMATION; HYDRATION; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTON TRANSPORT; SIMULATION; STRUCTURE ACTIVITY RELATION; TEMPERATURE;

EID: 0033181018     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990801)36:2<175::AID-PROT4>3.3.CO;2-I     Document Type: Article

References (59)

1. Sosnick TR, Mayne L, Hiller R, Englander SW. The barriers in protein folding Nat Struct Biol 1994;1:149-156.
2. Elove GA, Bhuyan AK, Roder H. Kinetic mechanisms of cytochrome c folding: involvement of the heme and its ligands. Biochemistry 1994;33:6925-6935.
3. Yeh S-R, Takahashi S, Fan B, Rousseau DL. Ligand exchange during cytochrome c folding Nat Struct Biol 1997;4:51-56.
4. Pascher T, Chesick JP, Winkler JR, Gray HB. Protein folding triggered by electron transfer. Science 1996;271:1558-1560.
5. Mines GA, Pascher T, Lee SC, Winkler JR, Gray HB. Cytochrome c folding triggered by electron transfer. Chem Biol 1996;3:491-497.
6. Shastry MCR, Roder H. Evidence for barrier-limited protein folding kinetics on the microsecond time scale. Nat Struct Biol 1998;5:385-392.
7. Onuchic JN, Luthey-Schulten Z, Wolynes PG. Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem 1997;48:545-600.
8. Fersht AR. Nucleation mechanisms in protein folding Curr Opin Struct Biol 1997;7:3-9.
9. Northrup SH, Pear MP, McCammon JA, Karplus M. Molecular dynamics of ferrocytochrome c. Nature 1980;286:304-305.
10. Simonson T, Perahia D. Microscopic dielectric properties of cytochrome c from molecular dynamics simulations in acqueous solution. J Am Chem Soc 1995;117:7987-8000.
11. Muegge I, Qi PX, Wand AJ, Chu ZT, Warshel A. The reorganization energy of cytochrome c revisited. J Phys Chem B 1997;101:825-836.
12. Onuchic JN, Beratan DN, Winkler JR, gray HB. Pathway analysis of protein electron-transfer reactions. Annu Rev Biophys Biomol Struct 1992;21:349-377.
13. Bai YW, Milne JS, Mayne L, Englander SW. Primary structure effects on peptide group hydrogen exchange. Proteins 1993;17:75-86.
14. Bai YW, Milne JS, Mayne L, Englander SW. Protein stability parameters measured by hydrogen exchange. Proteins 1994;20:4-14.
15. Bai YW, Englander SW. Hydrogen bond strength and beta-sheet propensities - "the role of a side chanin blocking effect. Proteins 1994;18:262-266.
16. Bai YW, Sosnick TR, Mayne L, Englander SW. Protein folding intermediates: native-state hydrogen exchange. Science 1995;269: 192-197.
17. Bai YW, Englander SW. Future directions in folding: the multistate nature of protein structure. Proteins 1996;24:145-151.
18. Kallenbach NR. Breathing life into the folding pathway of cytochrome C. Nat Struct Biol 1995;2:813-816.
19. Xu Y, Mayne L, Englander SW. Evidence for an unfolding and refolding pathway in cytochrome c. Nat Struct Biol 1998;5:774-778.
20. Englander SW. Kallenbach NR. Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q Rev Biophys 1984;16:521-655.
21. Frauenfelder H, Sligar SG, Wolynes PG. The energy landscapes and motions of proteins. Science 1991;254:1598-1603.
22. García AE. Large-amplitude nonlinear motions in proteins. Phys Rev Lett 1992;68:2696-2699.
23. García AE, Soumpasis DM, Jovin TM. Dynamics and relative stabilities of parallel-and antiparallel-stranded DNA duplexes. Biophys J 1994;66:1742-1755.
24. 2 in non-crystalline environments show a subunit transition from the open to the closed conformation. Protein Sci 1996;5:62-71.
25. Gilmanshin R, Williams S, Callender RH, Woodruff WH, Dyer RB. Fast events in protein folding: relaxation dynamics of secondary and tertiary structure in native apomyoglobin Proc Natl Acad Sci USA 1997;94:3709-3713.
26. Hagen SJ, Hofrichter J, Eaton WA. Rate of interchain diffusion of unfolded cytochrome c. J Phys Chem 1997;101:2352-2365.
27. Ballew RM, Sabelko J, Gruebele M. Direct observation of fast protein folding: the initial collapse of apomyoglobin Proc Natl Acad Sci USA 1996;93:5759-5764.
28. Privalov PL. Cold denaturation of proteins. Crit Rev Biochem Mol Biol 1990;25:281-305.
29. Privalov PL, Makhatadze GI. Contribution of hydration to protein folding thermodynamics. 2. The entropy and gibbs energy of hydration. J Mol Biol 1993;232:660-679.
30. Garde S, Hummer G, García AE, Paulaitis ME, Pratt LR. Origin of entropy convergence in hydrophobic hydration and protein folding. Phys Rev Lett 1996;77:4966-4968.
31. Qi PX, DiStefano DL, Wand AJ. Solution structure of horse heart ferrocyctochrome c determined by high-resolution NMR and restrained simulated annealing. Biochemistry 1994;33:6408-6417.
32. Qi PXR, beckman RA, Wand AJ. Solution structure of horse heart ferricytochrome-c and detection of redox-related structural changes by high-resolution H-1-NMR. Biochemistry 1996;35:12275-12286.
33. Bushnell GW, Louie GV, Brayer GD. High-resolution 3-dimensional structure of horse heart cytochrome c. J Mol Biol 1990;214: 585-595.
34. Trewhella J, Carlson VAP, Curtis EH, Heidorn DB. Difference in the solution sturctures of oxydized and reduced cytochrome c measured by small-angle x-ray scattering. Biochemistry 1988;27: 1121-1125.
35. Banci L, Bertini I, Gray HB, et al. Solution structure of oxydized horse heart cytochrome c. Biochemistry 1997;1997;36:9867-9877.
36. Jones CM, Henry ER, Hu Y, et al. Fast events in protein folding initiated by nanosecond laser photolysis. Proc Natl Acad Sci USA 1993;90:11860-11864.
37. Hartshorn RT, Moore GR. A denaturation-induced proton-uptake study of horse ferricytochrome-c. Biochem J 1989;258:595-598.
38. Cornell WD, Cieplak P, Bayley CI, et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
39. Darden T, York D, Pedersen L. Particle mesh Ewald: an Nlog(N) method for Ewald sums in large systems. J Chem Phys 1993;98: 10089-10092.
40. Pearlman DA, Case DA, Caldwell JW, et al. AMBER, V. 4.1, 1995.
41. García AE, Hummer G, blumfield R, Krumhansl JA. Multi-basin dynamics of a protein in a crystal environment. Physica D 1997;107:225-239.
42. García AE. Multi-basin dynamics of a protein in acqueous solution. In Peyrard M, editor. Nonlinear excitations in biomolecules, les editions des physique. Berlin: Springer; 1995. p 191-208.
43. Amadei A, Linssen ABM, Berendsen HC. Essential dynamics of proteins. Proteins 1993;17:412-425.
44. Hayward S, Go N. Collective variable description of native protein dynamics. Annu Rev Phys Chem 1995;46:223.
45. Wang L, Chen RX, Kallenbach NR. Proteolysis as a probe of thermal unfolding of cytochrome c. Proteins 1998;30:435-441.
46. Fontana A, Zambonin M, De Filippis V, Bosco M, Polverino de Lareto P. Limited protoeolysis of cytochrome c in trifluoroethanol. FEBS Lett 1995;362:266-270.
47. Lazaridis T, Lee I, Karplus M. Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin. Protein Sci 1997;6:2589-2605.
48. Daggett V, Levitt M. Realistic simulations of native-protein dynamics in solution and beyond. Annu Rev Biophys Biomol Struct 1993;22:353-380.
49. Brooks CL. Simulations of protein-folding and unfolding. Curr Opin Struct Biol 1998;8:222-226.
50. Milne JS, Roder H, Wand AJ, Englander SW. Determinants of protein hydrogen exchange studied in equine cytochrome c. Protein Sci 1998;7:739-745.
51. García AE, Stiller L. Computation of the mean residence time of water in the hydration shells of biomolecules. J Comput Chem 1993;14:1396-1406.
52. Mehrotra PK. Beveridge DL. Structural analysis of molecular solutions based on quasi-component distribution-functions: application to [H2C0]aq at 25-degrees-c. J Amer Chem Soc 1980;102: 4287-4294.
53. Howry WA, Sauder JM, Roder H, Scheraga HA. Definition of amide protection factors for early kinetic intermediates in protein folding. Proc Natl Acad Sci USA 1998;95:4299-4302.
54. Levitt M, Sander C, Stern PS. Protein normal-mode dynamics: trypsinoinhibitor, crambin, ribonuclease and lysozyme. J Mol Biol 1985;181:423-447.
55. Klafter J, Shlesinger MF, Zumofen G. Beyond Brownian motion. Physics Today 1996;49:33-39.
56. Shlesinger MF, Zaslavsky GM, Klafter J. Strange kinetics. Nature 1993;363:31-37.
57. Ansari A, Berendzen J, Bowne SF, et al. Protein states and proteinquakes. Proc Natl Acad Sci USA 1985;82:5000-5004.
58. Bahar I, Wallquist A, Covel DG, Jernigan RL. Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry 1998;37:1067-1075.
59. García AE, Krumhansl JA, Frauenfelder H. Variations on a theme by Debye and Waller: from simple crystals to proteins. Proteins 1997;29:153-160.