Molecular dynamics of biomolecules through direct analysis of dipolar couplings

Journal of the American Chemical Society

Volumn 137, Issue 19, 2015, Pages 6270-6278

  Olsson, Simon ^a,b   Ekonomiuk, Dariusz ^a   Sgrignani, Jacopo ^a   Cavalli, Andrea ^a,c  

^a INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Switzerland)

^b ETH ZURICH   (Switzerland)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COUPLINGS; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; NUCLEIC ACIDS; TENSORS;

ALIGNMENT TENSORS; DIPOLAR COUPLINGS; DIRECT ANALYSIS; INTRINSICALLY DISORDERED PROTEINS; MAXIMUM ENTROPY PRINCIPLE; MULTI DOMAINS; RESIDUAL DIPOLAR COUPLING (RDCS); STRUCTURAL BIOLOGY;

MAXIMUM ENTROPY METHODS;

INTRINSICALLY DISORDERED PROTEIN; LYSOZYME; NUCLEIC ACID; ESCHERICHIA COLI PROTEIN; FKPA PROTEIN, E COLI; MEMBRANE PROTEIN; PEPTIDYLPROLYL ISOMERASE;

ARTICLE; BIOMOLECULE; CHEMICAL STRUCTURE; DECOMPOSITION; DENSITY; DIMERIZATION; ENTROPY; ENZYME ACTIVE SITE; MAGNETIC FIELD; MOLECULAR DYNAMICS; MOLECULE; NUCLEAR OVERHAUSER EFFECT; PROTEIN CONFORMATION; PROTEIN DATA BANK; PROTEIN EXPRESSION; PROTON NUCLEAR MAGNETIC RESONANCE; STRUCTURE ANALYSIS; ANIMAL; CHEMISTRY; CHICKEN; ESCHERICHIA COLI; NUCLEAR MAGNETIC RESONANCE;

ANIMALS; CHICKENS; ENTROPY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MEMBRANE PROTEINS; MOLECULAR DYNAMICS SIMULATION; MURAMIDASE; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDYLPROLYL ISOMERASE; PROTEIN CONFORMATION;

EID: 84930227396     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/jacs.5b01289     Document Type: Article

References (68)

1. Karplus, M.; Kuriyan, J. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6679-85
2. Fenwick, R. B.; Esteban-Martín, S.; Richter, B.; Lee, D.; Walter, K. F. A.; Milovanovic, D.; Becker, S.; Lakomek, N. A.; Griesinger, C.; Salvatella, X. J. Am. Chem. Soc. 2011, 133, 10336-9
3. Pitera, J. W.; Chodera, J. D. J. J. Chem. Theory Comput. 2012, 8, 3445
4. Roux, B.; Weare, J. J. Chem. Phys. 2013, 138, 084107
5. Cavalli, A.; Camilloni, C.; Vendruscolo, M. J. Chem. Phys. 2013, 138, 094112
6. Olsson, S.; Frellsen, J.; Boomsma, W.; Mardia, K. V.; Hamelryck, T. PLoS One 2013, 8, e79439
7. Olsson, S.; Vögeli, B. R.; Cavalli, A.; Boomsma, W.; Ferkinghoff-Borg, J.; Lindorff-Larsen, K.; Hamelryck, T. J. Chem. Theory Comput. 2014, 10, 3484-3491
8. Beauchamp, K. A.; Pande, V. S.; Das, R. Biophys. J. 2014, 106, 1381-90
9. Lindorff-Larsen, K.; Best, R. B.; Depristo, M. A.; Dobson, C. M.; Vendruscolo, M. Nature 2005, 433, 128-32
10. Vögeli, B.; Kazemi, S.; Güntert, P.; Riek, R. Nat. Struct. Mol. Biol. 2012, 19, 1053-7
11. Henzler-Wildman, K.; Kern, D. Nature 2007, 450, 964-72
12. Bouvignies, G.; Bernadó, P.; Meier, S.; Cho, K.; Grzesiek, S.; Brüschweiler, R.; Blackledge, M. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13885-90
13. Clore, G. M.; Schwieters, C. D. J. Mol. Biol. 2006, 355, 879-86
14. de Simone, A.; Montalvao, R. W.; Dobson, C. M.; Vendruscolo, M. Biochemistry 2013, 52, 6480-6
15. Thaning, J.; Stevensson, B.; Ostervall, J.; Naidoo, K. J.; Widmalm, G.; Maliniak, A. J. Phys. Chem. B 2008, 112, 8434-6
16. Showalter, S. A.; Brüschweiler, R. J. Am. Chem. Soc. 2007, 129, 4158-4159
17. Lange, O. F.; Lakomek, N.-A.; Farès, C.; Schröder, G. F.; Walter, K. F. A.; Becker, S.; Meiler, J.; Grubmüller, H.; Griesinger, C.; de Groot, B. L. Science 2008, 320, 1471-5
18. Esteban-Martín, S.; Fenwick, R. B.; Salvatella, X. J. Am. Chem. Soc. 2010, 132, 4626-32
19. Fisher, C. K.; Huang, A.; Stultz, C. M. J. Am. Chem. Soc. 2010, 132, 14919-27
20. Prestegard, J. H.; al Hashimi, H. M.; Tolman, J. R. Q. Rev. Biophys. 2000, 33, 371-424
21. Bax, A. Protein Sci. 2003, 12, 1-16
22. Tolman, J. R.; Flanagan, J. M.; Kennedy, M. A.; Prestegard, J. H. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 9279-83
23. Yao, L.; Bax, A. J. Am. Chem. Soc. 2007, 129, 11326-7
24. Higman, V. A.; Boyd, J.; Smith, L. J.; Redfield, C. J. Biomol. NMR 2011, 49, 53-60
25. Saupe, A. Naturforscher 1964, 19a, 161-171
26. Salvatella, X.; Richter, B.; Vendruscolo, M. J. Biomol. NMR 2008, 40, 71-81
27. Hu, K.; Galius, V.; Pervushin, K. Biochemistry 2006, 45, 11983-91
28. Sanchez-Martinez, M.; Crehuet, R. Phys. Chem. Chem. Phys. 2014, 16, 26030-9
29. Marsh, J. A.; Baker, J. M. R.; Tollinger, M.; Forman-Kay, J. D. J. Am. Chem. Soc. 2008, 130, 7804-5
30. Salmon, L.; Nodet, G.; Ozenne, V.; Yin, G.; Jensen, M. R.; Zweckstetter, M.; Blackledge, M. J. Am. Chem. Soc. 2010, 132, 8407-18
31. Camilloni, C.; Vendruscolo, M. J. Phys. Chem. B 2015, 119, 653-661
32. Catalano, D.; Forte, C.; Veracini, C. A.; Zannoni, C. Isr. J. Chem. 1983, 23, 283-289
33. Catalano, D.; di Bari, L.; Veracini, C. A.; Shilstone, G. N.; Zannoni, C. J. Chem. Phys. 1991, 94, 3928-3935
34. Catalano, D.; Emsley, J. W.; la Penna, G.; Veracini, C. A. J. Chem. Phys. 1996, 105, 10595-10605
35. Berardi, R.; Spinozzi, F.; Zannoni, C. J. Chem. Phys. 1998, 109, 3742-3759
36. Stevensson, B.; Sandström, D.; Maliniak, A. J. Chem. Phys. 2003, 119, 2738-2746
37. Celebre, G.; Cinacchi, G. J. Chem. Phys. 2006, 124, 176101
38. Thiele, C. M.; Schmidts, V.; Böttcher, B.; Louzao, I.; Berger, R.; Maliniak, A.; Stevensson, B. Angew. Chem., Int. Ed. Engl. 2009, 48, 6708-12
39. Jaynes, E. T. In Probability Theory: The Logic of Science; Bretthorst, G. L., Ed.; Cambridge University Press: Cambridge, U.K., 2003.
40. Stevensson, B.; Landersjö, C.; Widmalm, G.; Maliniak, A. J. Am. Chem. Soc. 2002, 124, 5946-5947
41. Landersjö, C.; Stevensson, B.; Eklund, R.; Ostervall, J.; Söderman, P.; Widmalm, G.; Maliniak, A. J. Biomol. NMR 2006, 35, 89-101
42. Boomsma, W.; Ferkinghoff-Borg, J.; Lindorff-Larsen, K. PLoS Comput. Biol. 2014, 10, e1003406
43. Clore, G. M.; Gronenborn, A. M.; Tjandra, N. J. Magn. Reson. 1998, 131, 159-62
44. Habeck, M.; Nilges, M.; Rieping, W. J. Biomol. NMR 2008, 40, 135-44
45. Agmon, N.; Alhassid, Y.; Levine, R. J. Comput. Phys. 1979, 30, 250-258
46. Procaccia, I.; Shimoni, Y.; Levine, R. D. J. Chem. Phys. 1976, 65, 3284-3301
47. Alhassid, Y.; Agmon, N.; Levine, R. Chem. Phys. Lett. 1978, 53, 22-26
48. Fu, B.; Sahakyan, A. B.; Camilloni, C.; Tartaglia, G. G.; Paci, E.; Caflisch, A.; Vendruscolo, M.; Cavalli, A. J. Comput. Chem. 2014, 35, 1101-1105
49. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. J. Comput. Chem. 2003, 24, 1999-2012
50. Onufriev, A.; Case, D. A.; Bashford, D. J. Comput. Chem. 2002, 23, 1297-304
51. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. J. Comput. Phys. 1977, 23, 327-341
52. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690
53. Schwalbe, H.; Grimshaw, S. B.; Spencer, A.; Buck, M.; Boyd, J.; Dobson, C. M.; Redfield, C.; Smith, L. J. Protein Sci. 2001, 10, 677-88
54. Saul, F. A.; Arié, J.-P.; Vulliez-le Normand, B.; Kahn, R.; Betton, J.-M.; Bentley, G. A. J. Mol. Biol. 2004, 335, 595-608
55. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J. Chem. Phys. 1953, 21, 1087-1092
56. Habeck, M. Phys. Rev. E 2014, 89, 052113
57. Losonczi, J. A.; Andrec, M.; Fischer, M. W.; Prestegard, J. H. J. Magn. Reson. 1999, 138, 334-342
58. Yao, L.; Vögeli, B.; Ying, J.; Bax, A. J. Am. Chem. Soc. 2008, 130, 16518-20
59. McCammon, J. A.; Gelin, B. R.; Karplus, M.; Wolynes, P. G. Nature 1976, 262, 325-6
60. Smith, L. J.; Sutcliffe, M. J.; Redfield, C.; Dobson, C. M. Biochemistry 1991, 30, 986-996
61. Lindorff-Larsen, K.; Best, R. B.; Vendruscolo, M. J. Biomol. NMR 2005, 32, 273-280
62. Louhivuori, M.; Otten, R.; Lindorff-Larsen, K.; Annila, A. J. Am. Chem. Soc. 2006, 128, 4371-6
63. Tapley, T. L.; Körner, J. L.; Barge, M. T.; Hupfeld, J.; Schauerte, J. A.; Gafni, A.; Jakob, U.; Bardwell, J. C. A. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 5557-62
64. Quan, S.; Wang, L.; Petrotchenko, E. V.; Makepeace, K. A.; Horowitz, S.; Yang, J.; Zhang, Y.; Borchers, C. H.; Bardwell, J. C. Elife 2014, 3, e01584
65. Quan, S.; Koldewey, P.; Tapley, T.; Kirsch, N.; Ruane, K. M.; Pfizenmaier, J.; Shi, R.; Hofmann, S.; Foit, L.; Ren, G.; Jakob, U.; Xu, Z.; Cygler, M.; Bardwell, J. C. A. Nat. Struct. Mol. Biol. 2011, 18, 262-9
66. Humphrey, W.; Dalke, A.; Schulten, K. J. Molec. Graphics 1996, 14, 33-38
67. Boomsma, W. J. Comput. Chem. 2013, 34, 1697-1705
68. Tribello, G. A.; Bonomi, M.; Branduardi, D.; Camilloni, C.; Bussi, G. Comput. Phys. Commun. 2014, 185, 604-613