Unfolding of Globular Proteins: Monte Carlo Dynamics of a Realistic Reduced Model

Biophysical Journal

Volumn 85, Issue 5, 2003, Pages 3271-3278

  Kolinski, Andrzej ^a,b   Klein, Piotr ^a   Romiszowski, Piotr ^a   Skolnick, Jeffrey ^b  

^a UNIVERSITY OF WARSAW   (Poland)

^b UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBULAR PROTEIN;

ARTICLE; CORRELATION ANALYSIS; CRYSTALLOGRAPHY; MOLECULAR MODEL; MONTE CARLO METHOD; PREDICTION; PROTEIN FOLDING; PROTEIN STRUCTURE; TEMPERATURE;

EID: 0242322468     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74745-6     Document Type: Article

References (44)

1. Bernstein, F. C., T. F. Koetzle, G. J. B. Williams, E. F. Meyer, Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Simanouchi, and M. Tasumi. 1977. The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542.
2. Blanco, F., G. Rivas, and L. Serrano. 1994. A short linear peptide that folds into a native stable β-hairpin in aqueous solution. Struct. Biol. 1:584-590.
3. Blanco, J. F., and L. Serrano. 1995. Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements. Eur. J. Biochem. 230:634-649.
4. Blundell, T. L., and L. N. Johnson. 1976. Protein Crystallography. Academic Press, London, UK.
5. Branden, C., and J. Tooze. 1991. Introduction to Protein Structure. Garland Publishing, New York and London.
6. Cavagnero, S., H. J. Dyson, and P. E. Wright. 1999. Effect of H-helix destabilizing mutations on the kinetic and equilibrium folding of apomyoglobin. J. Mol. Biol. 285:269-282.
7. Clementi, C., A. Garcia, and J. N. Onuchic. 2003. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: an all-atom representation study. J. Mol. Biol. 326:933-954.
8. Creighton, T. E. 1990. Protein folding. Biochem. J. 270:1-16.
9. Ding, F., N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich. 2002. Direct molecular dynamics observation of protein folding transition state ensemble. Biophys. J. 83:3525-3532.
10. Dyson, H. J., J. R. Sayre, H.-C. Shin, G. S. Merutka, R. A. Lerner, and P. E. Wright. 1992. Conformational studies of complete proteins as a series of fragments using proton nuclear magnetic resonance spectroscopy. II. Plastocyanin. J. Mol. Biol. 226:819-835.
11. Eliezer, D., and P. E. Wright. 1996. Is apomyoglobin a molten globule? Structural characterization by NMR. J. Mol. Biol. 263:531-538.
12. Frank, M. K., G. M., Clore, and A. M. Gronenborn. 1995. Structural and dynamic characterization of the urea denatured state of the immunoglobulin binding domain of streptococcal protein G by multidimensional heteronuclear NMR spectroscopy. Protein Sci. 4:2605-2615.
13. Gilmanshin, R., S. Williams, H. R. Callender, and W. H. Woodruff. 1997. Fast events in protein folding: relaxation dynamics of secondary and tertiary structure in native apomyoglobin. Biophysics. 94:3709-3713.
14. Go, N., H. Abe, H. Mizuno, and H. Taketomi (editors). 1980. Protein Folding. Elsevier/North-Holland, Amsterdam, The Netherlands. 167-181.
15. Gronenborn, A., D. R. Filpula, N. Z. Essig, A. Achari, M. Whitlow, P. T. Wingfield, and G. M. Clore. 1991. A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science. 253:657-660.
16. Guo, C., M. S. Cheung, H. Levine, and D. A. Kessler. 2002. Mechanism underlying sequence-independent beta-sheet formation. J. Chem. Phys. 116:4353-4365.
17. Haliloglu, T., and I. Bahar. 1998. Coarse-grained simulations of conformational dynamics of proteins: application to apomyoglobin. Proteins. 31:271-281.
18. Ilkowski, B., J. Skolnick, and A. Kolinski. 2000. Helix-coil and β-sheet-coil transitions in a simplified protein model. Macromol. Theory Simulat. 9:523-533.
19. Irback, A., F. Sjunnesson, and S. Wallin. 2000. Three-helix-bundle protein in a Ramachandran model. Proc. Natl. Acad. Sci. USA. 97:13614-13618.
20. Jennings, P. A., and P. E. Wright. 1993. Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin. Science. 262:892-896.
21. Karanicolas, J., and C. L. Brooks III. 2002. The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci. 11:2351-2361.
22. Kihara, D., H. Lu, A. Kolinski, and J. Skolnick. 2001. TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc. Natl. Acad. Sci. USA. 99:5993-5998.
23. Klimov, D. K., and D. Thirumalai. 2000. Mechanisms and kinetics of β-hairpin formation. Proc. Natl. Acad. Sci. USA. 97:2544-2549.
24. Kolinski, A., M. Betancourt, D. Kihara, P. Rotkiewicz, and J. Skolnick. 2001. Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, lattice and off-lattice modeling for protein structure prediction and refinement. Proteins. 44:133-149.
25. Kolinski, A., B. Ilkowski, and J. Skolnick. 1999. Folding dynamics and thermodynamics of β-hairpin assembly: insight from various simulation techniques. Biophys. J. 77:2942-2952.
26. Kolinski, A., P. Rotkiewicz, B. Ilkowski, and J. Skolnick. 2000. Protein folding: flexible lattice models. Progr. Theor. Phys. (Kyoto). 138:S292-S300.
27. Kolinski, A., and J. Skolnick. 1996. Lattice Models of Protein Folding, Dynamics and Thermodynamics, R.G. Landes, Austin, TX.
28. Kolinski, A., and J. Skolnick. 1998. Assembly of protein structure from sparse experimental data: an efficient Monte Carlo model. Proteins. 32:475-494.
29. Kuszewski, J., G. M. Clore, and A. M. Gronenborn. 1994. Fast folding of a protolypic polypeptide: the immunoglobin binding domain of streptococcal protein G. Protein Sci. 3:1945-1952.
30. Liwo, A., C. Czaplewski, J. Pilardy, and H. A. Scheraga. 2001. Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field. J. Chem. Phys. 115:2323-2347.
31. McCallister, E. L., E. Alm, and D. Baker. 2000. Critical role of β-hairpin formation in protein G folding. Nat. Struct. Biol. 7:669-673.
32. Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys. 51:1087-1092.
33. Munoz, V., P. A. Thompson, J. Hofrichter, and W. A. Eaton. 1997. Folding dynamics and mechanism of β-hairpin formation. Nature. 390:196-197.
34. Nishimura, C., S. Prytulla H. J. Dyson, and P. E. Wright. 2000. Conservation of folding pathways in evolutionary distant globin sequences. Nat. Struct. Biol. 7:679-686.
35. Reymond, M. T., G. Merutka, H. J. Dyson, and P. E. Wright. 1997. Folding propensities of peptide fragments of myoglobin. Protein Sci. 6:706-716.
36. Rost, B., and C. Sander. 1994. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins. 19: 55-72.
37. Shea, J.-E., and C. L. Brooks III. 2000. 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. Sheinerman, F. B., and C. L. Brooks III. 1998. Calculations on folding of segment B1 of streptococcal protein G. J. Mol. Biol. 278:439-456.
39. Skolnick, J., A. Kolinski, and A. R. Ortiz. 2000. Derivation of protein-specific pair potentials based on weak sequence fragment similarity. Proteins. 38:3-16.
40. Takada, S., Z. Luthey-Schulten, and P. G. Wolynes. 1999. Folding dynamics with nonadditive force. A simulation study of designed helical protein and a random heteropolymer. J. Chem. Phys. 110:11616-11629.
41. Tcherkasskaya, O., and V. N. Uversky. 2001. Denatured collapsed states in protein folding: example of apomyoglobin. Proteins. 44:244-254.
42. Wagner, U. G., N. Moeiler, W. Schmitzberger, H. Falk, and C. Kratky. 1995. Structure determination of the biliverdin apomyoglobin complex: crystal structure analysis of two crystal forms at 1.4 and 1.5 Å resolution. J. Mol. Biol. 247:326-337.
43. Wikstrom, M., U. Sjobring, W. Kastern, L. Bjorck, T. Drakenberg, and S. Forsen. 1993. Proton nuclear magnetic resonance sequential assignments and secondary structure of an immunoglobulin light chain-binding domain of protein L. Biochemistry. 32:3381-3386.
44. Wright, P. E., H. J. Dyson, and R. A. Lerner. 1988. Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding. Biochemistry. 37:7167-7175.