Global stability of protein folding from an empirical free energy function

Journal of Theoretical Biology

Volumn 321, Issue , 2013, Pages 44-53

  Ruiz Blanco, Yasser B ^a   Marrero Ponce, Yovani ^a,b   Paz, Waldo ^a   García, Yamila ^b,c   Salgado, Jesús ^b  

^a CENTRAL UNIVERSITY OF LAS VILLAS   (Cuba)

^b UNIVERSITY OF VALENCIA   (Spain)

^c CATALAN INSTITUTE OF NANOSCIENCE AND NANOTECHNOLOGY ICN2   (Spain)

Author keywords

Empirical potential for proteins; Prediction of protein folding stability; PROTCAL

Indexed keywords

BIOPHYSICS; DECOMPOSITION ANALYSIS; EMPIRICAL ANALYSIS; HYDROPHOBICITY; MODELING; PROTEIN;

ANALYTICAL PARAMETERS; ARTICLE; BIOENERGY; BIOPHYSICS; DECOMPOSITION; DISPERSION; ENTROPY; HYDROPHOBICITY; PHYSICAL CHEMISTRY; PREDICTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEIN UNFOLDING; PROTHERM DATABASE; STATIC ELECTRICITY; STRUCTURE ANALYSIS;

ALGORITHMS; DATABASES, PROTEIN; LINEAR MODELS; MODELS, STATISTICAL; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; REPRODUCIBILITY OF RESULTS; SOFTWARE; THERMODYNAMICS;

EID: 84873869799     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2012.12.023     Document Type: Article

References (45)

1. Anfinsen C.B., Scheraga H.A. Experimental and theoretical aspects of protein folding. Adv. Protein Chem. 1975, 29:205-300.
2. Anfinsen C.B. Principles that govern the folding of protein chains. Science 1973, 181:223-230.
3. Baker D. A surprising simplicity to protein folding. Nature 2000, 405:39-42.
4. Beglov D., Roux B. J. Chem. Phys. 1994, 100:9050-9063.
5. Bogatyreva N.S., Osypov A.A., Ivankov D.N. KineticDB: a database of protein folding kinetics. Nucleic Acids Res. 2009, 37:D342-D346.
6. Bava K.A., Gromiha M.M., Uedaira H., Kitajima K., Sarai A. ProTherm, version 4.0: thermodynamic database for proteins and mutants. Nucleic Acids Res. 2004, 32:D120-D121.
7. Clementi C., García A.E., Onuchic J.N. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L. J. Mol. Biol. 2003, 326:933-954.
8. Collet O. How does the first water shell fold proteins so fast?. J. Chem. Phys. 2011, 134. 085107-085107.
9. Collantes E.R., Dunn-III W.J. Amino acid side chain descriptors for quantitative structure-activity relationship studies of peptide analogues. J. Med. Chem. 1995, 38:2705-2713.
10. Dill K.A. Polymer principles and protein folding. Protein Sci. 1999, 8:1166-1180.
11. Dill K.A., Chan H.S. From Levinthal to pathways to funnels. Nat. Struct. Biol. 1997, 4:10-19.
12. Dobson C.M., Sali A., Karplus M. Protein folding: a perspective from theory and experiment. Angew. Chem. Int. Ed. Engl. 1998, 37:868-893.
13. Dill K.A. Dominant forces in protein folding. Biochemistry 1990, 29:7133-7155.
14. Essex J.W., Jorgensen W.L. J. Comput. Chem. 1995, 16:951-972.
15. Gromiha M.M. Prediction of protein stability upon point mutations. Biochem. Soc. Trans. 2007, 35:1569-1573.
16. Guerois R., Nielsen J.E., Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol. 2002, 320:369-387.
17. Ghosh, K., Dill, K.A., 2009. Computing protein stabilities from their chain lengths. In: Proceedings of the National Academy of Sciences.
18. Honig B. Protein folding: from the Levinthal paradox to structure prediction. J. Mol. Biol. 1999, 293:283-293.
19. Jiang L., Kuhlman B., Kortemme T., Baker D. A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. PROTEINS: structure, function, and bioinformatics 2005, 58:893-904.
20. Jackson S.E. How do small single-domain proteins fold?. Folding & Design 1998, 3:R81-R91.
21. Kinjo A.R., Miyazawa S. On the optimal contact potential of proteins. Chem. Phys. Lett. 2008, 451:132-135.
22. Kloss E., Courtemanche N., Barrick D. Repeat-protein folding: new insights into origins of cooperativity, stability, and topology. Arch. Biochem. Biophys. 2008, 469:83-99.
23. Kauzmann W. Some factors in the interpretation of protein denaturation. Advan. Protein Chem. 1959, 14:1-63.
24. Kauzmann W. The Mechanism of Enzyme Action 1954, 40. Johns Hopkins University Press, Baltimore. W.D. McElroy, B. Glass (Eds.).
25. Levine R.D., Bernstein R.B. Molecular reaction dynamics and chemical reactivity 1987, Oxford Univ Press, New York.
26. Maisuradze G.G., Senet P., Czaplewski C., Liwo A., Scheraga H.A. Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J. Phys. Chem. A 2010, 114:4471-4485.
27. Maxwell K.L., Wildes D., Afsar A.Z., Rios M.A.D.L., Brown A.G.T.C., Friel Hedberg.L., Horng J.C., Bona D., Miller E.J., Bélisle A.V., Main E.R.G., Bemporad F., Qiu L., Teilum K., Vu N.D., Edwards A.M., Ruczinski I., Poulsen F.M., Kragelund B.B., Michnick S.W., Chiti F., Bai Y., Hagen S.J., Serrano L., Oliveberg M., Raleigh D.P., Stafshede P.W., Radford S.E., Jackson S.E., Sosnick T.R., Marqusee S., Davidson A.R., Plaxco K.W. Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci. 2005, 14:602-616.
28. Matthews B.W. Studies on protein stability with T4 lysozyme. Adv. Protein Chem. 1995, 46:249-278.
29. Matthews B.W. Structural and genetic analysis of protein stability. Annu. Rev. Biochem. 1993, 62:139-160.
30. Ma B.G., Chen L.L., Zhang H.Y. What determines protein folding type? An investigation of intrinsic structural properties and its implications for understanding folding mechanisms. J. Mol. Biol. 2007, 370:439-448.
31. Nicholls A., Sharp K.A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. PROTEINS: Structure, Function, and Genetics 1991, 11:281-296.
32. Prusiner S.B. Prion protein biology. Cell 1998, 93:337-348.
33. Plaxco K.W., Simons K.T., Ruczinski I., Baker D. Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry 2000, 39:11177-11183.
34. Pauling L., Corey R.B. The pleated sheet, a new layer configuration of polypeptide chains. Proc. Nat. Acad. Sci. USA 1951, 37:251-256.
35. Roterman I.K., Lambert M.H., Gibson K.D., Scheraga H.A. A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. PHI-PSI maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests. J. Biomol. Struct. Dyn. 1998, 7:421-453.
36. Rhee Y.M., Sorin E.J., Jayachandran G., Lindahl E., Pande V.S. Simulations of the role of water in the protein folding mechanism. PNAS 2004, 101:6456-6461.
37. Ruiz-Blanco, Y.B., Paz, W., Marrero-Ponce, Y., Quiteros, I.M., PROTCAL, Santa Clara 2012.
38. Shakhnovich E.I. Theoretical studies of protein-folding thermodynamics and kinetics. Curr. Opin. Struct. Biol. 1997, 7:29-40.
39. Scott L.P.B., Chahine J., Ruggiero J.R. Use of genetic algorithms and solvation potential to study peptides structure. Appl. Math. Comput. 2008, 195:515-522.
40. Shakhnovich E.I. Modeling protein folding: the beauty and power of simplicity. Folding & Design 1996, 1:R50-R54.
41. Schymkowitz J., Borg J., Stricher F., Nys R., Rousseau F., Serrano L. The FoldX web server: an online force field. Nucleic Acids Res. 2005, 33:382-388.
42. Tanford C. Contribution of hydrophobic interactions to the stability of the globular conformation of proteins. J. Am. Chem. Soc. 1962, 84:4240-4247.
43. van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hunenberger, P.H., Kruger, P., Mark, A.E., Scott, W.R.P., Tironi, I.G., Biomolecular simulation: The GROMOS96 Manual and User Guide, Vdf Hochschulverlag AG an der ETH Zurich, Zurich 1996.
44. Wales D.J., Scheraga H.A. Global optimization of clusters, crystals, and biomolecules. Science 1999, 285:1368-1372.
45. Yang A.S., Sharp K., Honig B. Analysis of the heat capacity dependence of protein folding. J. Mol. Biol. 1992, 227:889-900.