Protein dynamics, thermal stability, and free-energy landscapes: A molecular dynamics investigation

Biophysical Journal

Volumn 85, Issue 4, 2003, Pages 2641-2649

  Tavernelli, Ivano ^a,b   Cotesta, Simona ^a,c   Di Iorio, Ernesto E ^a  

^a ETH ZURICH   (Switzerland)

^b Institut de chimie moleculaire et biologique Ecole Polytechnique Federale de Lausanne   (Switzerland)

^c PFIZER INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; CHEMICAL BINDING; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; ENERGY; LANDSCAPE; MOLECULAR DYNAMICS; MOLECULAR STABILITY; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; THERMOSTABILITY;

GOES;

EID: 0141707867     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74687-6     Document Type: Article

References (19)

1. Amadei, A., A. B. M. Linssen, B. L. deGroot, D. M. F. vanAalten, and H. J. C. Berendsen. 1996. An efficient method for sampling the essential subspace of proteins. J. Biomol. Struct. Dyn. 13:615-625.
2. Ansari, A., J. Berendzen, S. F. Bowne, H. Frauenfelder, I. E. Iben, T. B. Sauke, E. Shyamsunder, and R. D. Young. 1985. Protein states and proteinquakes. Proc. Natl. Acad. Sci. USA. 82:5000-5004.
3. Bryngelson, J. D., J. N. Onuchic, N. D. Socci, and P. G. Wolynes, 1995. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins. 21:167-195.
4. Bryngelson, J. D., and P. G. Wolynes. 1987. Spin glasses and the statistical mechanics of protein folding. Proc. Natl. Acad. Sci. USA. 84:7524-7528.
5. Cotesta, S., I. Tavernelli, and E. E. Di Iorio. 2003. Dynamics of RNase-A and S-protein: a molecular dynamics simulation of the transition toward a folding intermediate. Biophys. J. 85:2633-2640.
6. Di Iorio, E. E., I. Tavernelli, and W. Yu. 1997. Dynamic properties of the monomeric insect erythrocruorin-III from Chironomus thummi-thummi. Relationships between structural flexibility and functional complexity. Biophys. J. 73:2742-2751.
7. Eidsness, M. K., K. A. Richie, A. E. Burden, D. M. J. Kurtz, and R. A. Scott. 1997. Dissecting contributions to the thermostability of Pyrococcus furiosus rubredoxin: beta-sheet chimeras. Biochemistry. 36:10406-10413.
8. Kirkpatrick, T. R., and D. Thirumalai. 1988. Comparison between dynamical theories and metastable states in regular and glassy meanfield spin models with underlying first-order-like phase transition. Phys. Rev. A. 37:4439-4448.
9. Lazaridis, T., G. Archontis, and M. Karplus. 1995. Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics. In Advances in Protein Chemistry. Academic Press, San Diego, CA. 231-306.
10. Leopold, E. L., M. Montal, and J. N. Onuchic. 1992. Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proc. Natl. Acad. Sci. USA. 89:8721-8725.
11. Onuchic, J. N., P. G. Wolynes, Z. Luthey-Schulten, and N. D. Socci. 1995. Toward an outline of the topography of a realistic protein-folding funnel. Proc. Natl. Acad. Sci. USA. 92:3626-3630.
12. Pliska, P., and E. Marinari. 1993. On heteroplymer shape dynamics. Europhysics Lett. 22:167-173.
13. Plotkin, S. S., J. Wang, and P. G. Wolynes. 1997. Statistical mechanics of a correlated energy landscape model for protein folding funnels. J. Chem. Phys. 106:2932-2948.
14. Szilágyi, A., and P. Závodszky. 2000. Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Structure. 8:493-504.
15. Tavernelli, I., and E. E. Di Iorio. 2001. The interplay between protein dynamics and frustration of non-bonded interactions as revealed by molecular dynamics simulations. Chem. Phys. Lett. 345:287-294.
16. van Gunsteren, W. F., S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, A. E. Scott, and I. G. Tironi. 1996. Biomolecular Simulation: The GROMOS96 Manual and User Guide. VDF Hochschulverlag AG an der ETH Zürich, Zürich.
17. Watts, D. J., and S. H. Strogatz. 1998. Collective dynamics of 'small-world' networks. Nature (Lond.). 393:440-442.
18. Wolynes, P. G., and W. A. Eaton. 1999. The physics of protein folding. Physics World. 12:39-44.
19. Wolynes, P. G., Z. Luthey-Schulten, and J. N. Onuchic. 1996. Fast folding experiments and the topography of protein folding energy landscapes. Chemistry & Biology. 3:425-432.