Automated NMR relaxation dispersion data analysis using NESSY

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Bieri, Michael ^a   Gooley, Paul R ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

s ms motion; Conformational chemical exchange; Cpmg; Protein dynamics; Software; Transition state theory; Van't hoff

Indexed keywords

CPMG; LEVENBERG-MARQUARDT MINIMIZATION; NMR RELAXATION DISPERSION; NUCLEAR MAGNETIC RESONANCE(NMR); PROTEIN DYNAMICS; RELAXATION DISPERSION; TRANSITION STATE THEORIES; VAN'T HOFF;

COMPUTER SOFTWARE; EXPERIMENTS; PROTEINS; SOFTWARE ENGINEERING;

DISPERSIONS;

PROTEIN;

ARTICLE; CHEMISTRY; COMPUTER LANGUAGE; COMPUTER PROGRAM; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE IMAGING; PROTEIN CONFORMATION;

MAGNETIC RESONANCE IMAGING; MOLECULAR DYNAMICS SIMULATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROGRAMMING LANGUAGES; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 80054938897     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-421     Document Type: Article

References (22)

1. Grzesiek S, Sass HJ. From biomolecular structure to functional understanding: new NMR developments narrow the gap. Curr Opin Struct Biol 2009, 19(5):585-595. 10.1016/j.sbi.2009.07.015, 19716691.
2. Cabodi S, Di Stefano P, Leal Mdel P, Tinnirello A, Bisaro B, Morello V, Damiano L, Aramu S, Repetto D, Tornillo G, et al. Integrins and signal transduction. Adv Exp Med Biol 2010, 674:43-54. 10.1007/978-1-4419-6066-5_5, 20549939.
3. Johnson-Winters K, Tollin G, Enemark JH. Elucidating the catalytic mechanism of sulfite oxidizing enzymes using structural, spectroscopic, and kinetic analyses. Biochemistry 2010, 49(34):7242-7254. 10.1021/bi1008485, 2927705, 20666399.
4. Tabernero L, Aricescu AR, Jones EY, Szedlacsek SE. Protein tyrosine phosphatases: structure-function relationships. FEBS J 2008, 275(5):867-882. 10.1111/j.1742-4658.2008.06251.x, 18298793.
5. Palmer AG. NMR probes of molecular dynamics: overview and comparison with other techniques. Annu Rev Biophys Biomol Struct 2001, 30:129-155. 10.1146/annurev.biophys.30.1.129, 11340055.
6. O'Connell NE, Grey MJ, Tang Y, Kosuri P, Miloushev VZ, Raleigh DP, Palmer AG. Partially folded equilibrium intermediate of the villin headpiece HP67 defined by 13C relaxation dispersion. J Biomol NMR 2009, 45(1-2):85-98. 10.1007/s10858-009-9340-0, 2810208, 19644656.
7. Wang C, Grey MJ, Palmer AG. CPMG sequences with enhanced sensitivity to chemical exchange. J Biomol NMR 2001, 21(4):361-366. 10.1023/A:1013328206498, 11824755.
8. Loria JP, Berlow RB, Watt ED. Characterization of enzyme motions by solution NMR relaxation dispersion. Acc Chem Res 2008, 41(2):214-221. 10.1021/ar700132n, 18281945.
9. Cavanagh J, Venters RA. Protein dynamic studies move to a new time slot. Nat Struct Biol 2001, 8(11):912-914. 10.1038/nsb1101-912, 11685230.
10. Brath U, Akke M. Differential responses of the backbone and side-chain conformational dynamics in FKBP12 upon binding the transition-state analog FK506: implications for transition-state stabilization and target protein recognition. J Mol Biol 2009, 387(1):233-244. 10.1016/j.jmb.2009.01.047, 19361439.
11. Baldwin AJ, Kay LE. NMR spectroscopy brings invisible protein states into focus. Nat Chem Biol 2009, 5(11):808-814. 10.1038/nchembio.238, 19841630.
12. Peng JW. Communication breakdown: protein dynamics and drug design. Structure 2009, 17(3):319-320. 10.1016/j.str.2009.02.004, 19278644.
13. Luz Z, Meiboom S. Nuclear magnetic resonance study of protolysis of trimethylammonium ion in aqueous solution - order of reaction with respect to solvent. Journal of Chemical Physics 1963, 39(2):366.
14. Carver JP, Richards RE. General 2-site solution for chemical exchange produced dependence of T2 upon carr-purcell pulse separation. Journal of Magnetic Resonance 1972, 6(1):89.
15. Demers JP, Mittermaier A. Binding mechanism of an SH3 domain studied by NMR and ITC. J Am Chem Soc 2009, 131(12):4355-4367. 10.1021/ja808255d, 19267471.
16. d'Auvergne EJ, Gooley PR. The use of model selection in the model-free analysis of protein dynamics. J Biomol NMR 2003, 25(1):25-39. 10.1023/A:1021902006114, 12566997.
17. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 1995, 6(3):277-293.
18. Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED. The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 2005, 59(4):687-696. 10.1002/prot.20449, 15815974.
19. Escoubas P, De Weille JR, Lecoq A, Diochot S, Waldmann R, Champigny G, Moinier D, Menez A, Lazdunski M. Isolation of a tarantula toxin specific for a class of proton-gated Na+ channels. J Biol Chem 2000, 275(33):25116-25121. 10.1074/jbc.M003643200, 10829030.
20. Kovrigin EL, Kempf JG, Grey MJ, Loria JP. Faithful estimation of dynamics parameters from CPMG relaxation dispersion measurements. Journal of Magnetic Resonance 2006, 180(1):93-104. 10.1016/j.jmr.2006.01.010, 16458551.
21. Johnson BA, Blevins RA. NMR View - a computer-program for the visualization and analysis of nmr data. J Biomol NMR 1994, 4(5):603-614.
22. Niedzwiecka A, Stepinski J, Darzynkiewicz E, Sonenberg N, Stolarski R. Positive heat capacity change upon specific binding of translation initiation factor eIF4E to mRNA 5' cap. Biochemistry 2002, 41(40):12140-12148. 10.1021/bi0258142, 12356315.