Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions

Journal of Chemical Physics

Volumn 139, Issue 12, 2013, Pages

  Gur, M ^a   Zomot, E ^a   Bahar, I ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

ANISOTROPY; LIPID BILAYERS; MAMMALS; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; PROTEINS;

ANISOTROPIC NETWORKS; BOVINE PANCREATIC TRYPSIN INHIBITORS; COMPARATIVE ANALYSIS; CONFORMATIONAL ENERGIES; GLUTAMATE TRANSPORTERS; MECHANISM OF FUNCTIONS; MOLECULAR BIOPHYSICS; MOLECULAR DYNAMICS SIMULATIONS;

CRYSTAL STRUCTURE;

AMINO ACID TRANSPORTER; APROTININ; ASPARTIC ACID; WATER; LIPID BILAYER;

ALGORITHM; ANIMAL; ANISOTROPY; ARTICLE; CATTLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; KINETICS; LIPID BILAYER; METABOLISM; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; TIME; BOVINAE;

ALGORITHMS; AMINO ACID TRANSPORT SYSTEMS; ANIMALS; ANISOTROPY; APROTININ; ASPARTIC ACID; CATTLE; KINETICS; LIPID BILAYERS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PRINCIPAL COMPONENT ANALYSIS; TIME FACTORS; WATER;

EID: 84885458692     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4816375     Document Type: Article

References (58)

1. A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar, Biophys. J. 80, 505 (2001). 10.1016/S0006-3495(01)76033-X
2. I. Bahar, T. R. Lezon, L. W. Yang, and E. Eyal, Annu. Rev. Biophys. 39, 23 (2010). 10.1146/annurev.biophys.093008.131258
3. A. Bakan and I. Bahar, Proc. Natl. Acad. Sci. U.S.A. 106, 14349 (2009). 10.1073/pnas.0904214106
4. D. Tobi and I. Bahar, Proc. Natl. Acad. Sci. U.S.A. 102, 18908 (2005). 10.1073/pnas.0507603102
5. O. Keskin, BMC Struct. Biol. 7, 31 (2007). 10.1186/1472-6807-7-31
6. A. Grossfield, S. E. Feller, and M. C. Pitman, Proteins 67, 31 (2007). 10.1002/prot.21308
7. T. D. Romo and A. Grossfield, Proteins 79, 23 (2011). 10.1002/prot.22855
8. R. O. Dror, M. O. Jensen, and D. E. Shaw, Conf. Proc. IEEE Eng. Med. Biol. Soc. 2009, 2340 (2009). 10.1109/IEMBS.2009.5335057
9. J. L. Klepeis, K. Lindorff-Larsen, R. O. Dror, and D. E. Shaw, Curr. Opin. Struct. Biol. 19, 120 (2009). 10.1016/j.sbi.2009.03.004
10. D. E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R. O. Dror, M. P. Eastwood, J. A. Bank, J. M. Jumper, J. K. Salmon, Y. B. Shan, and W. Wriggers, Science 330, 341 (2010). 10.1126/science.1187409
11. E. Zomot and I. Bahar, J. Biol. Chem. 288, 8231 (2013). 10.1074/jbc.M112.438432
12. G. E. Torres and S. G. Amara, Curr. Opin. Neurobiol. 17, 304 (2007). 10.1016/j.conb.2007.05.002
13. S. G. Amara, Nature (London) 360, 420 (1992). 10.1038/360420d0
14. E. Zomot, A. Bakan, I. H. Shrivastava, J. DeChancie, T. R. Lezon, and I. Bahar, Sodium-coupled Secondary Transporters, Molecular Machines (World Scientific Publishing Co. Pte. Ltd., 2011), p. 199.
15. D. Yernool, O. Boudker, Y. Jin, and E. Gouaux, Nature (London) 431, 811 (2004). 10.1038/nature03018
16. M. Karplus and J. A. McCammon, Nat. Struct. Biol. 9, 646 (2002). 10.1038/nsb0902-646
17. J. A. McCammon, B. R. Gelin, and M. Karplus, Nature (London) 267, 585 (1977). 10.1038/267585a0
18. D. van der Spoel, A. R. van Buuren, D. P. Tieleman, and H. J. Berendsen, J. Biomol. NMR 8, 229 (1996). 10.1007/BF00410322
19. S. Swaminathan, T. Ichiye, W. Van Gunsteren, and M. Karplus, Biochemistry 21, 5230 (1982). 10.1021/bi00264a019
20. M. Levitt, Nature (London) 294, 379 (1981). 10.1038/294379a0
21. M. Levitt and R. Sharon, Proc. Natl. Acad. Sci. U.S.A. 85, 7557 (1988). 10.1073/pnas.85.20.7557
22. R. M. Brunne and W. F. van Gunsteren, FEBS Lett. 323, 215 (1993). 10.1016/0014-5793(93)81342-W
23. C. L. Brooks III, A. Brunger, and M. Karplus, Biopolymers 24, 843 (1985). 10.1002/bip.360240509
24. B. Brooks and M. Karplus, Proc. Natl. Acad. Sci. U.S.A 80, 6571 (1983). 10.1073/pnas.80.21.6571
25. N. Go, T. Noguti, and T. Nishikawa, Proc. Natl. Acad. Sci. U.S.A. 80, 3696 (1983). 10.1073/pnas.80.12.3696
26. S. Hayward, A. Kitao, and N. Go, Protein Sci. 3, 936 (1994). 10.1002/pro.5560030608
27. M. Levitt, C. Sander, and P. S. Stern, J. Mol. Biol. 181, 423 (1985). 10.1016/0022-2836(85)90230-X
28. T. Nishikawa and N. Go, Proteins 2, 308 (1987). 10.1002/prot.340020407
29. M. S. Appavou, G. Gibrat, and M. C. Bellissent-Funel, Biochim. Biophys. Acta 1764, 414 (2006). 10.1016/j.bbapap.2006.01.010
30. S. Cusack, J. Smith, J. Finney, B. Tidor, and M. Karplus, J. Mol. Biol. 202, 903 (1988). 10.1016/0022-2836(88)90566-9
31. K. Wuthrich and G. Wagner, FEBS Lett. 50, 265 (1975). 10.1016/0014-5793(75)80504-7
32. G. Wagner, D. Bruhwiler, and K. Wuthrich, J. Mol. Biol. 196, 227 (1987). 10.1016/0022-2836(87)90524-9
33. G. Otting, E. Liepinsh, and K. Wuthrich, Biochemistry 32, 3571 (1993). 10.1021/bi00065a008
34. G. Verdon and O. Boudker, Nat. Struct. Mol. Biol. 19, 355 (2012). 10.1038/nsmb.2233
35. O. Boudker, R. M. Ryan, D. Yernool, K. Shimamoto, and E. Gouaux, Nature (London) 445, 387 (2007). 10.1038/nature05455
36. N. Reyes, C. Ginter, and O. Boudker, Nature (London) 462, 880 (2009). 10.1038/nature08616
37. J. DeChancie, I. H. Shrivastava, and I. Bahar, Mol. Biosyst. 7, 832 (2011). 10.1039/C0MB00175A
38. T. R. Lezon and I. Bahar, Biophys. J. 102, 1331 (2012). 10.1016/j.bpj.2012.02.028
39. Z. Huang and E. Tajkhorshid, Biophys. J. 95, 2292 (2008). 10.1529/biophysj.108.133421
40. S. Stolzenberg, G. Khelashvili, and H. Weinstein, J. Phys. Chem. B 116, 5372 (2012). 10.1021/jp301726s
41. J. Jiang, I. H. Shrivastava, S. D. Watts, I. Bahar, and S. G. Amara, Proc. Natl. Acad. Sci. U.S.A. 108, 15141 (2011). 10.1073/pnas.1112216108
42. I. H. Shrivastava, J. Jiang, S. G. Amara, and I. Bahar, J. Biol. Chem. 283, 28680 (2008). 10.1074/jbc.M800889200
43. Y. Gu, I. H. Shrivastava, S. G. Amara, and I. Bahar, Proc. Natl. Acad. Sci. U.S.A. 106, 2589 (2009). 10.1073/pnas.0812299106
44. B. H. Leighton, R. P. Seal, S. D. Watts, M. O. Skyba, and S. G. Amara, J. Biol. Chem. 281, 29788 (2006). 10.1074/jbc.M604991200
45. V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling, Proteins 65, 712 (2006). 10.1002/prot.21123
46. H. W. Horn, W. C. Swope, J. W. Pitera, J. D. Madura, T. J. Dick, G. L. Hura, and T. Head-Gordon, J. Chem. Phys. 120, 9665 (2004). 10.1063/1.1683075
47. R. W. Pastor and A. D. MacKerell Jr., J. Phys. Chem. Lett. 2, 1526 (2011). 10.1021/jz200167q
48. O. Guvench and A. D. MacKerell Jr., Methods Mol. Biol. 443, 63 (2008). 10.1007/978-1-59745-177-2-4
49. A. Amadei, A. B. M. Linssen, and H. J. C. Berendsen, Proteins 17, 412 (1993). 10.1002/prot.340170408
50. Q. Cui and I. Bahar, Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems (Chapman & Hall, 2005).
51. F. Tama and Y. H. Sanejouand, Protein Eng. 14, 1 (2001). 10.1093/protein/14.1.1
52. L. Yang, G. Song, A. Carriquiry, and R. L. Jernigan, Structure (London) 16, 321 (2008). 10.1016/j.str.2007.12.011
53. See supplementary material at http://dx.doi.org/10.1063/1.4816375 E-JCPSA6-139-014336 for additional figures and tables.
54. A. Wlodawer, J. Walter, R. Huber, and L. Sjolin, J. Mol. Biol. 180, 301 (1984). 10.1016/S0022-2836(84)80006-6
55. B. Isin, K. Schulten, E. Tajkhorshid, and I. Bahar, Biophys. J. 95, 789 (2008). 10.1529/biophysj.107.120691
56. L. Liu, A. M. Gronenborn, and I. Bahar, Proteins 80, 616 (2011). 10.1002/prot.23225
57. Z. Yang, P. Majek, and I. Bahar, PLoS Comput. Biol. 5, e1000360 (2009). 10.1371/journal.pcbi.1000360
58. Y. Arkun and M. Gur, PLoS ONE 7, e29628 (2012). 10.1371/journal.pone. 0029628