Geometric Approximation: A New Computational Approach to Characterize Protein Dynamics from NMR Adiabatic Relaxation Dispersion Experiments

Journal of the American Chemical Society

Volumn 138, Issue 23, 2016, Pages 7337-7345

  Chao, Fa An ^a   Byrd, R Andrew ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; DIFFERENTIAL EQUATIONS; DYNAMICS; NUMERICAL METHODS;

ADIABATIC RELAXATION DISPERSIONS; COMPUTATIONAL STRATEGY; CONFORMATIONAL EXCHANGE; CONFORMATIONAL FLUCTUATIONS; EXPERIMENTAL VALIDATIONS; GEOMETRIC APPROXIMATIONS; NUMERICAL INTEGRATIONS; NUMERICAL SOLUTIONS OF DIFFERENTIAL EQUATIONS;

DISPERSIONS;

PROTON; UBIQUITIN CONJUGATING ENZYME;

ADIABATIC RELAXATION DISPERSION; ADIABATICITY; ANALYTIC METHOD; ARTICLE; CONFORMATIONAL TRANSITION; DISPERSION; GEOMETRIC APPROXIMATION METHOD; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; QUANTITATIVE ANALYSIS; QUANTUM MECHANICS; SIMULATION; VELOCITY; BIOLOGY; CHEMISTRY; COMPUTER SIMULATION; KINETICS; PROCEDURES; PROTEIN CONFORMATION; THEORETICAL MODEL;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; KINETICS; MODELS, THEORETICAL; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTONS; UBIQUITIN-CONJUGATING ENZYMES;

EID: 84975045637     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/jacs.6b02786     Document Type: Article

References (34)

1. Frederick, K. K.; Marlow, M. S.; Valentine, K. G.; Wand, A. J. Nature 2007, 448, 325 10.1038/nature05959
2. Boehr, D. D.; McElheny, D.; Dyson, H. J.; Wright, P. E. Science 2006, 313, 1638 10.1126/science.1130258
3. Popovych, N.; Sun, S.; Ebright, R. H.; Kalodimos, C. G. Nat. Struct. Mol. Biol. 2006, 13, 831 10.1038/nsmb1132
4. Phillips, A. H.; Schoeffler, A. J.; Matsui, T.; Weiss, T. M.; Blankenship, J. W.; Zobel, K.; Giannetti, A. M.; Dueber, E. C.; Fairbrother, W. J. Nat. Struct. Mol. Biol. 2014, 21, 1068 10.1038/nsmb.2916
5. Bhabha, G.; Lee, J.; Ekiert, D. C.; Gam, J.; Wilson, I. A.; Dyson, H. J.; Benkovic, S. J.; Wright, P. E. Science 2011, 332, 234 10.1126/science.1198542
6. Tzeng, S. R.; Kalodimos, C. G. Nature 2009, 462, 368 10.1038/nature08560
7. Mulder, F. A.; Mittermaier, A.; Hon, B.; Dahlquist, F. W.; Kay, L. E. Nat. Struct. Biol. 2001, 8, 932 10.1038/nsb1101-932
8. Palmer, A. G.; Kroenke, C. D.; Loria, J. P. Methods Enzymol. 2001, 339, 204 10.1016/S0076-6879(01)39315-1
9. Massi, F.; Grey, M. J.; Palmer, A. G., III Protein Sci. 2005, 14, 735 10.1110/ps.041139505
10. Davis, D. G.; Perlman, M. E.; London, R. E. J. Magn. Reson., Ser. B 1994, 104, 266 10.1006/jmrb.1994.1084
11. Luz, Z.; Meiboom, S. J. Chem. Phys. 1963, 39, 366 10.1063/1.1734254
12. Carver, J. P.; Richards, R. E. J. Magn. Reson. 1972, 6, 89 10.1016/0022-2364(72)90090-X
13. Trott, O.; Palmer, A. G. J. Magn. Reson. 2002, 154, 157 10.1006/jmre.2001.2466
14. Trott, O.; Abergel, D.; Palmer, A. G. Mol. Phys. 2003, 101, 753 10.1080/0026897021000054826
15. Mangia, S.; Traaseth, N. J.; Veglia, G.; Garwood, M.; Michaeli, S. J. Am. Chem. Soc. 2010, 132, 9979 10.1021/ja1038787
16. Mcconnell, H. M. J. Chem. Phys. 1958, 28, 430 10.1063/1.1744152
17. Mangia, S.; Liimatainen, T.; Garwood, M.; Michaeli, S. Magn. Reson. Imaging 2009, 27, 1074 10.1016/j.mri.2009.05.023
18. Traaseth, N. J.; Chao, F. A.; Masterson, L. R.; Mangia, S.; Garwood, M.; Michaeli, S.; Seelig, B.; Veglia, G. J. Magn. Reson. 2012, 219, 75 10.1016/j.jmr.2012.03.024
19. Goldman, M. J. Magn. Reson. 1984, 60, 437 10.1016/0022-2364(84)90055-6
20. Redfield, A. G. IBM J. Res. Dev. 1957, 1, 19 10.1147/rd.11.0019
21. Phillips, A. H.; Zhang, Y.; Cunningham, C. N.; Zhou, L.; Forrest, W. F.; Liu, P. S.; Steffek, M.; Lee, J.; Tam, C.; Helgason, E.; Murray, J. M.; Kirkpatrick, D. S.; Fairbrother, W. J.; Corn, J. E. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 11379 10.1073/pnas.1302407110
22. Houben, K.; Dominguez, C.; van Schaik, F. M.; Timmers, H. T.; Bonvin, A. M.; Boelens, R. J. Mol. Biol. 2004, 344, 513 10.1016/j.jmb.2004.09.054
23. Das, R.; Mariano, J.; Tsai, Y. C.; Kalathur, R. C.; Kostova, Z.; Li, J.; Tarasov, S. G.; McFeeters, R. L.; Altieri, A. S.; Ji, X.; Byrd, R. A.; Weissman, A. M. Mol. Cell 2009, 34, 674 10.1016/j.molcel.2009.05.010
24. Delaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfeifer, J.; Bax, A. J. Biomol. NMR 1995, 6, 277 10.1007/BF00197809
25. Goddard, T. D.; Kneller, D. G. Sparky 3; University of California: San Francisco.
26. Bourbaki, N. General Topology; Addison-Wesley: Reading, MA, 1966.
27. Auer, R.; Tollinger, M.; Kuprov, I.; Konrat, R.; Kloiber, K. J. Biomol. NMR 2011, 51, 35 10.1007/s10858-011-9539-8
28. Metropolis, N.; Ulam, S. J. Am. Stat. Assoc. 1949, 44, 335 10.1080/01621459.1949.10483310
29. Bieri, M.; Gooley, P. R. BMC Bioinf. 2011, 12, 421 10.1186/1471-2105-12-421
30. Abragam, A. Principles of Nuclear Magnetism; Oxford University Press: Oxford, U.K., 1961.
31. Lange, O. F.; Lakomek, N. A.; Fares, C.; Schroder, G. F.; Walter, K. F.; Becker, S.; Meiler, J.; Grubmuller, H.; Griesinger, C.; de Groot, B. L. Science 2008, 320, 1471 10.1126/science.1157092
32. Brzovic, P. S.; Lissounov, A.; Christensen, D. E.; Hoyt, D. W.; Klevit, R. E. Mol. Cell 2006, 21, 873 10.1016/j.molcel.2006.02.008
33. Das, R.; Liang, Y. H.; Mariano, J.; Li, J.; Huang, T.; King, A.; Tarasov, S. G.; Weissman, A. M.; Ji, X.; Byrd, R. A. EMBO J. 2013, 32, 2504 10.1038/emboj.2013.174
34. Metzger, M. B.; Liang, Y. H.; Das, R.; Mariano, J.; Li, S.; Li, J.; Kostova, Z.; Byrd, R. A.; Ji, X.; Weissman, A. M. Mol. Cell 2013, 50, 516 10.1016/j.molcel.2013.04.004