Dynamics of RNase-A and S-protein: A molecular dynamics simulation of the transition toward a folding intermediate

Biophysical Journal

Volumn 85, Issue 4, 2003, Pages 2633-2640

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

^a ETH ZURICH   (Switzerland)

^b PFIZER INC   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

RIBONUCLEASE A; VITRONECTIN;

ALPHA HELIX; ARTICLE; BETA SHEET; CATTLE; COMPUTER SIMULATION; CONTROLLED STUDY; ENDOPLASMIC RETICULUM; ENERGY; HYDROPHOBICITY; MOLECULAR DYNAMICS; NONHUMAN; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE;

BOS TAURUS; BOVINAE;

EID: 0141819131     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74686-4     Document Type: Article

References (22)

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. 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.
3. Chakshusmathi, G., S. Ratnaparkhi-Girish, P. K. Madhu, and R. Varadarajan. 1999. Native-state hydrogen-exchange studies of a fragment complex can provide structural information about the isolated fragments. Proc. Natl. Acad. Sci. USA. 96:7899-7904.
4. 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.
5. Ellgaard, L., M. Molinari, and A. Helenius. 1999. Setting the standards: quality control in the secretory pathway. Science. 286:1882-1888.
6. Fischer, K. H., and J. A. Hertz. 1991. Spin Glasses. Cambridge University Press, Cambridge UK.
7. Gerstein, M., J. Tsai, and M. Levitt. 1995. The volume of atoms on the protein surface calculated from simulation, using Voronoi polyhedra. J. Mol. Biol. 249:955-966.
8. Koradi, R., M. Billeter, and K. Wüthrich. 1996. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14:51-55.
9. Mezard, M., G. Parisi, and M. A. Virasoro. 1987. Spin Glass Theory and Beyond. Word Scientific, Singapore.
10. Pliska, P., and E. Marinari. 1993. On heteroplymer shape dynamics. Europhysics Lett. 22:167-173.
11. Ritter, C. 2002. Characterization of the substrate properties recognized by the ER folding sensor UDP-glucose:glycoprotein glucosyltransferase. In Biology. Swiss Federal Institute of Technology-ETH, Zurich. 111.
12. Ritter, C., and A. Helenius. 2000. Recognition of local glycoprotein misfolding by the ER folding sensor UDP-glucose: glycoprotein glucosyltrasferase. Nat. Struct. Biol. 7:278-280.
13. Rosa, J. J., and F. M. Richards. 1981. Hydrogen exchange from identified regions of the S-protein component of ribonuclease as a function of temperature, pH, and the binding of S-peptide. J. Mol. Biol. 145:835-851.
14. Ryckaert, J.-P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
15. Sadoc, J.-F., and R. Mosseri. 1999. Geometrical Frustration. Cambridge University Press, Cambridge, UK. 307
16. Stella, L., M. Nicotra, G. Ricci, N. Rosato, and E. E. Di Iorio. 1999. Molecular dynamics simulations of human glutathione transferase P 1-1: analysis of the induced-fit mechanism by GST binding. Proteins. 37:1-9.
17. Tavernelli, I., S. Cotesta, and E. E. Di Iorio. 2003. Protein dynamics, thermal stability, and free energy landscapes: a molecular dynamics investigation. Biophys. J. 85:2641-2649.
18. 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.
19. Tironi, I. G., R. Sperb, P. E. Smith, and W. F. van Gunsteren. 1995. A generalized reaction field method for molecular dynamics simulations. J. Chem. Phys. 102:5451-5459.
20. 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.
21. Wolynes, P. G., and W. A. Eaton. 1999. The physics of protein folding. Physics World. 12:39-44.
22. 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.