Fast and accurate fitting of relaxation dispersion data using the flexible software package GLOVE

Journal of Biomolecular NMR

Volumn 56, Issue 3, 2013, Pages 275-283

  Sugase, Kenji ^b   Konuma, Tsuyoshi ^b   Lansing, Jonathan C ^c   Wright, Peter E ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b SUNTORY INSTITUTE FOR BIOORGANIC RESEARCH   (Japan)

^c Momenta Pharmaceuticals Inc   (United States)

Author keywords

Fitting software; Global fit; Local minimum problem; Monte Carlo minimization; Relaxation dispersion curve fitting; Speed and accuracy

Indexed keywords

ACCURACY; ARTICLE; COMPUTER PROGRAM; COST BENEFIT ANALYSIS; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MONTE CARLO METHOD; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; VELOCITY;

ALGORITHMS; MONTE CARLO METHOD; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84880137185     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-013-9747-5     Document Type: Article

References (25)

1. Bhabha G, Lee J, Ekiert DC, Gam J, Wilson IA, Dyson HJ, Benkovic SJ, Wright PE (2011) A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science 332:234-238
2. Bieri M, Gooley PR (2011) Automated NMR relaxation dispersion data analysis using NESSY. BMC Bioinformatics 12:421
3. Boehr DD, McElheny D, Dyson HJ, Wright PE (2006) The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313:1638-1642
4. Bouvignies G, Vallurupalli P, Hansen DF, Correia BE, Lange O, Bah A, Vernon RM, Dahlquist FW, Baker D, Kay LE (2011) Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature 477:111-114
5. 2 upon the Carr-Pursell pulse separation. J Magn Reson 6:89-105
6. Henzler-Wildman KA, Thai V, Lei M, Ott M, Wolf-Watz M, Fenn T, Pozharski E, Wilson MA, Petsko GA, Karplus M, Hübner CG, Kern D (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature 450:838-844
7. Hwang TL, van Zijl PC, Mori S (1998) Accurate quantitation of water-amide proton exchange rates using the phase-modulated CLEAN chemical EXchange (CLEANEX-PM) approach with a Fast-HSQC (FHSQC) detection scheme. J Biomol NMR 11:221-226
8. Ishima R, Torchia DA (2005) Error estimation and global fitting in transverse-relaxation dispersion experiments to determine chemical-exchange parameters. J Biomol NMR 32:41-54
9. Karplus M (2010) Dynamical aspects of molecular recognition. J Mol Recognit 23:102-104
10. Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Optimization by simulated annealing. Science 220:671-680
11. Kleckner IR, Foster MP (2011) GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data. J Biomol NMR 52:11-22
12. Li Z, Scheraga HA (1987) Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci USA 84:6611-6615
13. Loria JP, Rance M, Palmer AG (1999) A relaxation-compensated Carr-Purcell-Meiboom-Gill sequence for characterizing chemical exchange by NMR spectroscopy. J Am Chem Soc 121:2331-2332
14. Matsuki Y, Konuma T, Fujiwara T, Sugase K (2011) Boosting protein dynamics studies using quantitative nonuniform sampling NMR spectroscopy. J Phys Chem B 115:13740-13745
15. Meinhold DW, Wright PE (2011) Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion. Proc Natl Acad Sci USA 108:9078-9083
16. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller M, Teller E (1953) Equation of state calculations by very fast computing machines. J Chem Phys 21:1087-1092
17. Mosteller F, Tukey J (1968) Data analysis, including statistics. In: Lindzey G, Aronson E (eds) Handbook of social psychology, vol 2. Addison-Wesley, Reading, pp 80-203
18. Neudecker P, Robustelli P, Cavalli A, Walsh P, Lundström P, Zarrine-Afsar A, Sharpe S, Vendruscolo M, Kay LE (2012) Structure of an intermediate state in protein folding and aggregation. Science 336:362-366
19. Press WH, Teukolsky SA, Vetterling WT, Flannery BP (2007) Numerical recipes 3rd edition: the art of scientific computing. Cambridge University Press, Cambridge
20. 2H amide exchange NMR spectroscopy. J Mol Biol 380:726-741
21. Sugase K, Dyson HJ, Wright PE (2007a) Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447:1021-1025
22. Sugase K, Lansing JC, Dyson HJ, Wright PE (2007b) Tailoring relaxation dispersion experiments for fast-associating protein complexes. J Am Chem Soc 129:13406-13407
23. Tollinger M, Skrynnikov NR, Mulder FA, Forman-Kay JD, Kay LE (2001) Slow dynamics in folded and unfolded states of an SH3 domain. J Am Chem Soc 123:11341-11352
24. Vallurupalli P, Hansen DF, Kay LE (2008) Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy. Proc Natl Acad Sci USA 105:11766-11771
25. Yanagi K, Sakurai K, Yoshimura Y, Konuma T, Lee YH, Sugase K, Ikegami T, Naiki H, Goto Y (2012) The monomer-seed interaction mechanism in the formation of the β2-microglobulin amyloid fibril clarified by solution NMR techniques. J Mol Biol 422:390-402