1887
banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
The full text of this article is not currently available.
oa
Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions
Rent:
Rent this article for
Access full text Article
/content/aip/journal/jcp/139/12/10.1063/1.4816375
1.
1. A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar, Biophys. J. 80, 505 (2001).
http://dx.doi.org/10.1016/S0006-3495(01)76033-X
2.
2. I. Bahar, T. R. Lezon, L. W. Yang, and E. Eyal, Annu. Rev. Biophys. 39, 23 (2010).
http://dx.doi.org/10.1146/annurev.biophys.093008.131258
3.
3. A. Bakan and I. Bahar, Proc. Natl. Acad. Sci. U.S.A. 106, 14349 (2009).
http://dx.doi.org/10.1073/pnas.0904214106
4.
4. D. Tobi and I. Bahar, Proc. Natl. Acad. Sci. U.S.A. 102, 18908 (2005).
http://dx.doi.org/10.1073/pnas.0507603102
5.
5. O. Keskin, BMC Struct. Biol. 7, 31 (2007).
http://dx.doi.org/10.1186/1472-6807-7-31
6.
6. A. Grossfield, S. E. Feller, and M. C. Pitman, Proteins 67, 31 (2007).
http://dx.doi.org/10.1002/prot.21308
7.
7. T. D. Romo and A. Grossfield, Proteins 79, 23 (2011).
http://dx.doi.org/10.1002/prot.22855
8.
8. R. O. Dror, M. O. Jensen, and D. E. Shaw, Conf. Proc. IEEE Eng. Med. Biol. Soc. 2009, 2340 (2009).
http://dx.doi.org/10.1109/IEMBS.2009.5335057
9.
9. J. L. Klepeis, K. Lindorff-Larsen, R. O. Dror, and D. E. Shaw, Curr. Opin. Struct. Biol. 19, 120 (2009).
http://dx.doi.org/10.1016/j.sbi.2009.03.004
10.
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).
http://dx.doi.org/10.1126/science.1187409
11.
11. E. Zomot and I. Bahar, J. Biol. Chem. 288, 8231 (2013).
http://dx.doi.org/10.1074/jbc.M112.438432
12.
12. G. E. Torres and S. G. Amara, Curr. Opin. Neurobiol. 17, 304 (2007).
http://dx.doi.org/10.1016/j.conb.2007.05.002
13.
13. S. G. Amara, Nature (London) 360, 420 (1992).
http://dx.doi.org/10.1038/360420d0
14.
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.
15. D. Yernool, O. Boudker, Y. Jin, and E. Gouaux, Nature (London) 431, 811 (2004).
http://dx.doi.org/10.1038/nature03018
16.
16. M. Karplus and J. A. McCammon, Nat. Struct. Biol. 9, 646 (2002).
http://dx.doi.org/10.1038/nsb0902-646
17.
17. J. A. McCammon, B. R. Gelin, and M. Karplus, Nature (London) 267, 585 (1977).
http://dx.doi.org/10.1038/267585a0
18.
18. D. van der Spoel, A. R. van Buuren, D. P. Tieleman, and H. J. Berendsen, J. Biomol. NMR 8, 229 (1996).
http://dx.doi.org/10.1007/BF00410322
19.
19. S. Swaminathan, T. Ichiye, W. Van Gunsteren, and M. Karplus, Biochemistry 21, 5230 (1982).
http://dx.doi.org/10.1021/bi00264a019
20.
20. M. Levitt, Nature (London) 294, 379 (1981).
http://dx.doi.org/10.1038/294379a0
21.
21. M. Levitt and R. Sharon, Proc. Natl. Acad. Sci. U.S.A. 85, 7557 (1988).
http://dx.doi.org/10.1073/pnas.85.20.7557
22.
22. R. M. Brunne and W. F. van Gunsteren, FEBS Lett. 323, 215 (1993).
http://dx.doi.org/10.1016/0014-5793(93)81342-W
23.
23. C. L. Brooks III, A. Brunger, and M. Karplus, Biopolymers 24, 843 (1985).
http://dx.doi.org/10.1002/bip.360240509
24.
24. B. Brooks and M. Karplus, Proc. Natl. Acad. Sci. U.S.A 80, 6571 (1983).
http://dx.doi.org/10.1073/pnas.80.21.6571
25.
25. N. Go, T. Noguti, and T. Nishikawa, Proc. Natl. Acad. Sci. U.S.A. 80, 3696 (1983).
http://dx.doi.org/10.1073/pnas.80.12.3696
26.
26. S. Hayward, A. Kitao, and N. Go, Protein Sci. 3, 936 (1994).
http://dx.doi.org/10.1002/pro.5560030608
27.
27. M. Levitt, C. Sander, and P. S. Stern, J. Mol. Biol. 181, 423 (1985).
http://dx.doi.org/10.1016/0022-2836(85)90230-X
28.
28. T. Nishikawa and N. Go, Proteins 2, 308 (1987).
http://dx.doi.org/10.1002/prot.340020407
29.
29. M. S. Appavou, G. Gibrat, and M. C. Bellissent-Funel, Biochim. Biophys. Acta 1764, 414 (2006).
http://dx.doi.org/10.1016/j.bbapap.2006.01.010
30.
30. S. Cusack, J. Smith, J. Finney, B. Tidor, and M. Karplus, J. Mol. Biol. 202, 903 (1988).
http://dx.doi.org/10.1016/0022-2836(88)90566-9
31.
31. K. Wuthrich and G. Wagner, FEBS Lett. 50, 265 (1975).
http://dx.doi.org/10.1016/0014-5793(75)80504-7
32.
32. G. Wagner, D. Bruhwiler, and K. Wuthrich, J. Mol. Biol. 196, 227 (1987).
http://dx.doi.org/10.1016/0022-2836(87)90524-9
33.
33. G. Otting, E. Liepinsh, and K. Wuthrich, Biochemistry 32, 3571 (1993).
http://dx.doi.org/10.1021/bi00065a008
34.
34. G. Verdon and O. Boudker, Nat. Struct. Mol. Biol. 19, 355 (2012).
http://dx.doi.org/10.1038/nsmb.2233
35.
35. O. Boudker, R. M. Ryan, D. Yernool, K. Shimamoto, and E. Gouaux, Nature (London) 445, 387 (2007).
http://dx.doi.org/10.1038/nature05455
36.
36. N. Reyes, C. Ginter, and O. Boudker, Nature (London) 462, 880 (2009).
http://dx.doi.org/10.1038/nature08616
37.
37. J. DeChancie, I. H. Shrivastava, and I. Bahar, Mol. Biosyst. 7, 832 (2011).
http://dx.doi.org/10.1039/C0MB00175A
38.
38. T. R. Lezon and I. Bahar, Biophys. J. 102, 1331 (2012).
http://dx.doi.org/10.1016/j.bpj.2012.02.028
39.
39. Z. Huang and E. Tajkhorshid, Biophys. J. 95, 2292 (2008).
http://dx.doi.org/10.1529/biophysj.108.133421
40.
40. S. Stolzenberg, G. Khelashvili, and H. Weinstein, J. Phys. Chem. B 116, 5372 (2012).
http://dx.doi.org/10.1021/jp301726s
41.
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).
http://dx.doi.org/10.1073/pnas.1112216108
42.
42. I. H. Shrivastava, J. Jiang, S. G. Amara, and I. Bahar, J. Biol. Chem. 283, 28680 (2008).
http://dx.doi.org/10.1074/jbc.M800889200
43.
43. Y. Gu, I. H. Shrivastava, S. G. Amara, and I. Bahar, Proc. Natl. Acad. Sci. U.S.A. 106, 2589 (2009).
http://dx.doi.org/10.1073/pnas.0812299106
44.
44. B. H. Leighton, R. P. Seal, S. D. Watts, M. O. Skyba, and S. G. Amara, J. Biol. Chem. 281, 29788 (2006).
http://dx.doi.org/10.1074/jbc.M604991200
45.
45. V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling, Proteins 65, 712 (2006).
http://dx.doi.org/10.1002/prot.21123
46.
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).
http://dx.doi.org/10.1063/1.1683075
47.
47. R. W. Pastor and A. D. MacKerell Jr., J. Phys. Chem. Lett. 2, 1526 (2011).
http://dx.doi.org/10.1021/jz200167q
48.
48. O. Guvench and A. D. MacKerell Jr., Methods Mol. Biol. 443, 63 (2008).
http://dx.doi.org/10.1007/978-1-59745-177-2_4
49.
49. A. Amadei, A. B. M. Linssen, and H. J. C. Berendsen, Proteins 17, 412 (1993).
http://dx.doi.org/10.1002/prot.340170408
50.
50. Q. Cui and I. Bahar, Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems (Chapman & Hall, 2005).
51.
51. F. Tama and Y. H. Sanejouand, Protein Eng. 14, 1 (2001).
http://dx.doi.org/10.1093/protein/14.1.1
52.
52. L. Yang, G. Song, A. Carriquiry, and R. L. Jernigan, Structure (London) 16, 321 (2008).
http://dx.doi.org/10.1016/j.str.2007.12.011
53.
53.See supplementary material at http://dx.doi.org/10.1063/1.4816375 for additional figures and tables. [Supplementary Material]
54.
54. A. Wlodawer, J. Walter, R. Huber, and L. Sjolin, J. Mol. Biol. 180, 301 (1984).
http://dx.doi.org/10.1016/S0022-2836(84)80006-6
55.
55. B. Isin, K. Schulten, E. Tajkhorshid, and I. Bahar, Biophys. J. 95, 789 (2008).
http://dx.doi.org/10.1529/biophysj.107.120691
56.
56. L. Liu, A. M. Gronenborn, and I. Bahar, Proteins 80, 616 (2011).
http://dx.doi.org/10.1002/prot.23225
57.
57. Z. Yang, P. Majek, and I. Bahar, PLoS Comput. Biol. 5, e1000360 (2009).
http://dx.doi.org/10.1371/journal.pcbi.1000360
58.
58. Y. Arkun and M. Gur, PLoS ONE 7, e29628 (2012).
http://dx.doi.org/10.1371/journal.pone.0029628
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/12/10.1063/1.4816375
Loading
/content/aip/journal/jcp/139/12/10.1063/1.4816375
Loading

Data & Media loading...

Loading

Article metrics loading...

/content/aip/journal/jcp/139/12/10.1063/1.4816375
2013-07-26
2014-12-20

Abstract

The Anton supercomputing technology recently developed for efficient molecular dynamics simulations permits us to examine micro- to milli-second events at full atomic resolution for proteins in explicit water and lipid bilayer. It also permits us to investigate to what extent the collective motions predicted by network models (that have found broad use in molecular biophysics) agree with those exhibited by full-atomic long simulations. The present study focuses on Anton trajectories generated for two systems: the bovine pancreatic trypsin inhibitor, and an archaeal aspartate transporter, GltPh. The former, a thoroughly studied system, helps benchmark the method of comparative analysis, and the latter provides new insights into the mechanism of function of glutamate transporters. The principal modes of motion derived from both simulations closely overlap with those predicted for each system by the anisotropic network model (ANM). Notably, the ANM modes define the collective mechanisms, or the pathways on conformational energy landscape, that underlie the passage between the crystal structure and substates visited in simulations. In particular, the lowest frequency ANM modes facilitate the conversion between the most probable substates, lending support to the view that easy access to functional substates is a robust determinant of evolutionarily selected native contact topology.

Loading

Full text loading...

/deliver/fulltext/aip/journal/jcp/139/12/1.4816375.html;jsessionid=7fo81usc9rj02.x-aip-live-03?itemId=/content/aip/journal/jcp/139/12/10.1063/1.4816375&mimeType=html&fmt=ahah&containerItemId=content/aip/journal/jcp
true
true
This is a required field
Please enter a valid email address
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/12/10.1063/1.4816375
10.1063/1.4816375
SEARCH_EXPAND_ITEM