Role of electrostatic interactions for the stability and folding behavior of cold shock protein

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 9, 2010, Pages 2157-2169

  Su, Ji Guo ^a,b   Chen, Wei Zu ^a   Wang, Cun Xin ^a  

^a BEIJING UNIVERSITY OF TECHNOLOGY   (China)

^b YANSHAN UNIVERSITY   (China)

Author keywords

Folding kinetics; Folding unfolding pathway; Go model; Molecular dynamics; Thermophilic protein; Thermostability

Indexed keywords

COLD SHOCK PROTEIN; BACTERIAL PROTEIN; COLD SHOCK PROTEIN, BACILLUS; HEAT SHOCK PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; BACILLUS; BACILLUS CALDOLYTICUS; CARBOXY TERMINAL SEQUENCE; ENTHALPY; ENTROPY; MOLECULAR INTERACTION; MUTATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY; SIMULATION; STATIC ELECTRICITY; THERMODYNAMICS; WILD TYPE; CHEMISTRY; KINETICS; METABOLISM; MOLECULAR DYNAMICS;

BACILLUS CALDOLYTICUS;

BACTERIAL PROTEINS; HEAT-SHOCK PROTEINS; KINETICS; MOLECULAR DYNAMICS SIMULATION; MUTATION; PROTEIN FOLDING; PROTEIN STABILITY; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 77953592973     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22730     Document Type: Article

References (51)

1. Kumar S, Nussinov R. How do thermophilic proteins deal with heat? Cell Mol Life Sci 2001;58:1216-1233.
2. Querol E, Perez-Pons JA, Mozo-Villarias A. Analysis of protein conformational characteristics related to thermostability. Prot Eng Des Sel 1996;9:265-271.
3. Vogt G, Argos P. Protein thermo stability: hydrogen bonds or internal packing? Fold Des 1997;2:S40-S46.
4. Basu S, Sen S. Turning a mesophilic protein into a thermophilic one: a computational approach based on 3D structural features. J Chem Inf Model 2009;49:1741-1750.
5. Motono C, Gromiha MM, Kumar S. Thermodynamic and kinetic determinants of thermotoga maritima cold shock protein stability: a structural and dynamic analysis. Proteins 2008;71:655-669.
6. Karshikoff A, Ladenstein R. Ion pairs and the thermotolerance of proteins from hyperthermophiles: a "traffic rule" for hot roads. Trends Biochem Sci 2001;26:550-556.
7. Xiao L, Honig B. Electrostatic contributions to the stability of hyperthermophilic proteins. J Mol Biol 1999;289:1435-1444.
8. Karshikoff A, Ladenstein R. Proteins from thermophilic and mesophilic organisms essentially do not differ in packing. Prot Eng Des Sel 1998;11:867-872.
9. Dominy BN, Minoux H, Brooks CL, III. An electrostatic basis for the stability of thermophilic proteins. Proteins 2004;57:128-141.
10. Mueller U, Perl D, Schmid FX, Heinemann U. Thermo stability and atomic-resolution crystal structure of the Bacillus caldolyticus cold shock protein. J Mol Biol 2000;297:975-988.
11. Schindelin H, Marahiel MA, Heinemann U. Universal nucleic acidbinding domain revealed by crystal structure of the B. subtilis major cold shock protein. Nature 1993;364:164-168.
12. Schnuchel A, Wiltscheck R, Czisch M, Herrler M, Willinsky G, Graumann P, Marahiel MA, Holak TA, Structure in solution of the major cold-shock protein from Bacillus subtilis. Nature 1993;364: 169-171.
13. Perl D, Mueller U, Heinemann U, Schmid FX. Two exposed amino acid residues confer thermostability on a cold shock protein. Nat Struct Biol 2000;7:380-383.
14. Perl D, Holtermanu G, Schmid FX. Role of the chain termini for the folding transition state of the cold shock protein. Biochemistry 2001;40:15501-15511.
15. Martin A, Kather I, Schmid FX. Origins of the high stability of an in vitro-selected cold-shock protein. J Mol Biol 2002;318: 1341-1349.
16. Delbrück H, Mueller U, Perl D, Schmid FX, Heinemanu U. Crystal structures of mutant forms of the Bacillus caldolyticus cold shock protein differing in thermo stability. J Mol Biol 2001;313:359-369.
17. Perl D, Schmid FX. Electrostatic stabilization of a thermophilic cold shock protein. J Mol Biol. 2001;313:343-357.
18. Roca M, Messer B, Warshel A. Electrostatic contributions to protein stability and folding energy. FEBS Lett 2007;581:2065-2071.
19. Gribenko AV, Makhatadzd GI. Role of the charge-charge interactions in defining stability and halophilicity of the CspB proteins. J Mol Biol 2007;366:842-856.
20. Mozo-Villarias A, Cedano J, Querol E. A simple electrostatic criterion for predicting the thermal stability of proteins. Prot Eng Des Sel 2003;16:279-286.
21. Garofoli S, Falconi M, Desideri A. Thermophilicity of wild type and mutant cold shock proteins by molecular dynamics simulation. J Biomol Struct Dyn 2004;21:771-779.
22. Torrez M, Schultehenrich M, Livesay DR. Conferring thermostability to mesophilic proteins through optimized electrostatic surfaces. Biophys J 2003;85:2845-2853.
23. Zhou HX, Dong F. Electrostatic contributions to the stability of a thermophilic cold shock protein. Biophys J 2003;84:2216-2222.
24. Huang X, Zhou HX. Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulations. Biophys J 2006;91:2451-2463.
25. Garcia-Mira MM, Boehringer D, Schmid FX. The folding transition state of the cold shock protein is strongly polarized. J Mol Biol 2004;339:555-569.
26. Garcia-Mira MM, Schmid FX. Key role of coulombic interactions for the folding transition state of the cold shock protein. J Mol Biol 2006;364:458-468.
27. M orra G, Hodoscek M, Knapp EW. Unfolding of the cold shock protein studied with biased molecular dynamics. Proteins 2003;53:597-606.
28. Perl D, Welker C, Schindler T, Schröder K, Marahiel MA, Jaenicke R. Schmid FX Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins Nat Struct Biol 1998;5:229-235.
29. Bryngelson JD, Wolynes PG. Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci USA 1987;84:7524-7528.
30. Clementi C, Nymeyer H, Onuchic JN. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins J Mol Biol 2000;298:937-953.
31. Go N. Theoretical studies of protein folding. Annu Rev Biophys Bioeng 1983;12:183-210.
32. Weinkam P, Zong C, Wolynes PG. A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments. Proc Natl Acad Sci USA 2005;102:12401-12406.
33. Chavez LL, Gosavi S, Jennings PA, Onuchic JN. Multiple routes lead to the native state in the energy landscape of the beta-trefoil family. Proc Natl Acad Sci USA 2006;103:10254-10258.
34. Finke JM, Onuchic JN. Equilibrium and kinetic folding pathways of a TIM, barrel with a funneled energy landscape. Biophys J 2005;89: 488-505.
35. Kaya H, Chan HS. Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is nativecentric topological modeling? J Mol Biol 2003;326:911-931.
36. Szklarczyk O, Staron K, Cieplak M. Native state dynamics and mechanical properties of human topoisomerase 1 within a structure-based coarse-grained model. Proteins 2009;77:420-431.
37. Prieto L, Rey A. Influence of the native topology on the folding barrier for small proteins. J Chem Phys 2007;127:175101.
38. Wang W, Xu WX, Levy Y, Trizac E, Wolynes PG. Confinement effects on the kinetics and thermodynamics of protein dimerization. Proc Natl Acad Sci USA 2009;106:5517-5522.
39. Clementi C. Coarse-grained models of protein folding: toy-models or predictive tools? Curr Opin Struct Biol 2008;18:10-15.
40. Hills RD, Brooks CL. Insights from coarse-grained Go models for protein folding and dynamics. Int J Mol Sci 2009;10:889-905.
41. Zhang J, Li W, Wang J, Qin M, Wu L, Yan Z, Xu W, Zuo G, Wang W. Protein folding simulations: from coarse-grained model to allatom model. IUBMB Life 2009;61:627-643.
42. Levy Y, Onuchic JN, Wolynes PG. Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition. J Am Chem Soc 2007;129:738-739.
43. Cho SS, Weinkam P, Wolynes PG. Origins of barriers and barrierless folding in BBL. Proc Natl Acad Sci USA 2008;105:118-123.
44. Azia A, Levy Y. Nonnative electrostatic interactions can modulate protein folding: Molecular dynamics with a grain of salt. J Mol Biol 2009;393:527-542.
45. Givaty O, Levy Y. Protein sliding along DNA: dynamics and structural characterization. J Mol Biol 2009;385:1087-1097.
46. Veitshans T, Klimov D, Thirumalai D. Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequencedependent properties. Fold Des 1996;2:1-22.
47. Swope WC, Andersen HC, Berens PH, Wilson KR. A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: application to small water clusters. J Chem Phys 1982;76:637-649.
48. Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM. The weighted histogram analysis method for free-energy calculations on biomolecules. I: The method. J Comp Chem 1992;13: 1011-1021.
49. Ferrenberg AM, Swendsen RH. Optimized Monte-Carlo data analysis. Phys Rev Lett 1989;63:1195-1198.
50. Kouza M, Chang C, Hayryan S, Yu T, Li MS, Huang T, Hu C. Folding of the protein domain hbSBD. Biophys J 2005;89:3353-3361.
51. Qin M, Zhang J, Wang W. Effects of disulfide bonds on folding behavior and mechanism of the β-sheet protein tendamistat. Biophys J 2006;90:272-286.