Dynamics of the Hck-SH3 domain: Comparison of experiment with multiple molecular dynamics simulations

Protein Science

Volumn 9, Issue 1, 2000, Pages 95-103

  Horita, David A ^a   Zhang, Weixing ^b,c   Smithgall, Thomas E ^b,d   Gmeiner, William H ^b   Byrd, R Andrew ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

^c ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^d UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

15N relaxation; Conformational sampling; Molecular dynamics simulations; Order parameters; SH3 domain

Indexed keywords

ARTICLE; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; X RAY ANALYSIS;

EID: 0033979148     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.9.1.95     Document Type: Article

References (32)

1. Andrews BK, Romo T, Clarage JB, Pettitt BM, Phillips GN Jr. 1998. Characterizing the global substates of myoglobin. Structure 6:587-594.
2. Arold S, O'Brien R, Franken P, Strub M-P, Hoh F, Dumas C, Ladbury JE. 1998. RT loop flexibility enhances the specificity of Src family SH3 domains for HIV-1 Nef. Biochemistry 37:14683-14691.
3. Bevington PR, Robinson DK. 1992. Data reduction and error analysis for the physical sciences. Boston, Massachusetts: WCB/McGraw-Hill.
4. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M, 1983. CHARMm: A program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 4:187-217.
5. Brünger AT. 1987. X-PLOR version 3.1. A system for X-ray crystallography and NMR. New Haven, Connecticut: Yale University Press.
6. Byrd RA, Digennaro FS. 1995. A real-time in-line RF pulse sequence and acquisition monitor for NMR spectrometers. J Magn Reson Ser A 112:250-254.
7. Chandrasekhar I, Clore GM, Szabo A, Gronenborn AM, Brooks BR. 1992. A 500 ps molecular dynamics simulation study of interleukin-1β in water. Correlation with nuclear magnetic resonance spectroscopy and crystallography. J Mol Biol 226:239-250.
8. 13C NMR relaxation data. J Am Chem Soc 120:5301-5311.
9. Clore GM, Szabo A, Bax A, Kay LE, Driscoll PC, Gronenborn AM. 1990. Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation in proteins. J Am Chem Soc 112:4989-4991.
10. Cohen GB, Ren R, Baltimore D. 1995. Modular binding domains in signal transduction proteins. Cell 80:237-248.
11. Cooper A, Dryden DTF. 1984. Allostery without conformational change. Eur Biophys J 11:103-109.
12. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A. 1995. NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277-293.
13. Duan Y, Kollman PA. 1998. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282:740-744.
14. 15N NMR relaxation. Biochemistry 33:5984-6003.
15. Horita DA, Baldisseri DM, Zhang W, Altieri AS, Smithgall TE, Gmeiner WH, Byrd RA. 1998. Solution structure of the human Hck SH3 domain and identification of its ligand binding site. J Mol Biol 278:253-265.
16. Jorgensen WL, Chandrasekhar J, Medura JD, Impey RW, Klein ML. 1983. Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935.
17. Karplus M, McCammon JA. 1983. Dynamics of proteins: Elements and function. Annu Rev Biochem 53:263-300.
18. Lipari G, Szabo A. 1982a. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 104:4546-4559.
19. Lipari G, Szabo A. 1982b. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J Am Chem Soc 104:4559-4570.
20. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph D, et al. 1992. Self-consistent parameterization of biomolecules for molecular modeling and condensed phase simulations. FASEB J 6:A143.
21. Mandel AM, Akke M, Palmer AG III. 1995. Backbone dynamics of Escherichia coli ribonuclease HI: Correlations with structure and function in an active enzyme. J Mol Biol 246:144-163.
22. Palmer AG III. 1997. Probing molecular motion by NMR. Curr Opin Struct Biol 7:732-737.
23. 13C heteronuclear NMR spectroscopy. J Am Chem Soc 113:4371-4380.
24. Philippopoulos M, Lim C. 1995. Molecular dynamics simulation of E. coli ribonuclease H 1 in solution: Correlation with NMR and X-ray data and insights into biological function. J Mol Biol 254:771-792.
25. Philippopoulos M, Mandel AM, Palmer AG III, Lim C. 1997. Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics. Proteins 28:481-493.
26. Press WH, Flannery BP, Teukolsky SA, Vetterling WT. 1988. Numerical recipes in C. The Art of scientific computing. Cambridge, Massachusetts: Cambridge University Press.
27. Sicheri F, Moarefi I, Kuriyan J. 1997. Crystal structure of the Src family tyrosine kinase Hck. Nature 385:602-609.
28. Smith PE, Schaik RC, Szyperski T, Wüthrich K, van Gunsteren WF. 1995. Internal mobility of the basic pancreatic trypsin inhibitor in solution: A comparison of NMR spin relaxation measurements and molecular dynamics simulations. J Mol Biol 246:356-365.
29. Spolar RS, Record MT Jr. 1994. Coupling of local folding to site-specific binding of proteins to DNA. Science 263:777-784.
30. Steinbach PJ, Brooks BR. 1993. Protein hydration elucidated by molecular dynamics simulation. Proc Natl Acad Sci USA 90:9135-9139.
31. 15N NMR relaxation. J Am Chem Soc 117:12562-12566.
32. Weber G. 1975. Energetics of ligand binding to proteins. Adv Protein Chem 29:2-83.