Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers

Journal of Computational Chemistry

Volumn 35, Issue 4, 2014, Pages 300-308

  Li, Pai Chi ^a,b   Miyashita, Naoyuki ^b   Im, Wonpil ^c   Ishido, Satoshi ^a,d   Sugita, Yuji ^b  

^a RIKEN Center for Integrative Medical Sciences   (Japan)

^b RIKEN   (Japan)

^c UNIVERSITY OF KANSAS   (United States)

^d SHOWA PHARMACEUTICAL UNIVERSITY   (Japan)

Author keywords

glycophorin A; receptor tyrosine kinase EphA1; REMD; structure prediction; transmembrane helix dimer; umbrella sampling

Indexed keywords

GLYCOPHORIN A; RECEPTOR TYROSINE KINASE; REMD; STRUCTURE PREDICTION; TRANSMEMBRANE HELICES; UMBRELLA SAMPLING;

AMINO ACIDS; CELL MEMBRANES; CYTOLOGY; ENZYMES; FORECASTING; FREE ENERGY; MOLECULAR DYNAMICS; REACTION KINETICS; SIGNAL TRANSDUCTION;

DIMERS;

EPHRIN RECEPTOR A1; GLYCOPHORIN; GLYCOPHORIN A;

ARTICLE; CHEMISTRY; METABOLISM; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; RECEPTOR TYROSINE KINASE EPHA1; REMD; STRUCTURE PREDICTION; TRANSMEMBRANE HELIX DIMER; UMBRELLA SAMPLING;

GLYCOPHORIN A; RECEPTOR TYROSINE KINASE EPHA1; REMD; STRUCTURE PREDICTION; TRANSMEMBRANE HELIX DIMER; UMBRELLA SAMPLING;

GLYCOPHORIN; MOLECULAR DYNAMICS SIMULATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; RECEPTOR, EPHA1;

EID: 84891879962     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.23494     Document Type: Article

References (56)

1. K. C. Garcia, L. Teyton, I. A. Wilson, Annu. Rev. Immunol. 1999, 17, 369.
2. A. Ullrich, J. Schlessinger, Cell 1990, 61, 203.
3. D. M. Rosenbaum, S. G. F. Rasmussen, B. K. Kobilka, Nature 2009, 459, 356.
4. J. T. Parsons, A. R. Horwitz, M. A. Schwartz, Nat. Rev. Mol. Cell Biol. 2010, 11, 633.
5. G. Grigoryan, D. T. Moore, W. F. DeGrado, Annu. Rev. Biochem. 2011, 80, 211.
6. M. A. Lomize, A. L. Lomize, I. D. Pogozheva, H. I. Mosberg, Bioinformatics 2006, 22, 623.
7. G. E. Tusnády, Z. Dosztányi, I. Simon, Bioinformatics 2004, 20, 2964.
8. J. Zhu, B. H. Luo, P. Barth, J. Schonbrun, D. Baker, T. A. Springer, Mol. Cell 2009, 34, 234.
9. J. Yang, Y. Q. Ma, R. C. Page, S. Misra, E. F. Plow, J. Qin, Proc. Natl. Acad. Sci. USA 2009, 106, 17729.
10. T. L. Lau, C. Kim, M. H. Ginsberg, T. S. Ulmer, EMBO J. 2009, 28, 1351.
11. K. R. MacKenzie, J. H. Prestegard, D. M. Engelman, Science 1997, 276, 131.
12. S. O. Smith, D. Song, S. Shekar, M. Groesbeek, M. Ziliox, S. Aimoto, Biochemistry 2001, 40, 6553.
13. Y. Sugita, Y. Okamoto, Chem. Phys. Lett. 1999, 314, 141.
14. W. Im, M. Feig, C. L. Brooks, Biophys. J. 2003, 85, 2900.
15. H. Kokubo, Y. Okamoto, Chem. Phys. Lett. 2004, 383, 397.
16. L. Bu, W. Im, C. L. Brooks, III, Biophys. J. 2007, 92, 854.
17. N. Miyashita, J. E. Straub, D. Thirumalai, Y. Sugita, J. Am. Chem. Soc. 2009, 131, 3438.
18. G. M. Torrie, J. P. Valleau, J. Comput. Phys. 1977, 23, 187.
19. J. Gee, M. S. Shell, J. Chem. Phys. 2011, 134, 064112.
20. S. Park, T. Kim, W. Im, Phys. Rev. Lett. 2012, 108, 108102.
21. Z. Chen, Y. Xu, Proteins 2006, 62, 539.
22. S. Tanizaki, M. Feig, J. Chem. Phys. 2005, 122, 124706.
23. P. J. Bond, M. S. P. Sansom, J. Am. Chem. Soc. 2006, 128, 2697.
24. D. Sengupta, S. J. Marrink, Phys. Chem. Chem. Phys. 2010, 12, 12987.
25. J. Henin, A. Pohorille, C. Chipot, J. Am. Chem. Soc. 2005, 127, 8478.
26. W. Im, J. Lee, T. Kim, H. Rui, J. Comput. Chem. 2009, 30, 1622.
27. J. Lee, W. Im, J. Comput. Chem. 2007, 28, 669.
28. Y. Sugita, A. Kitao, Y. Okamoto, J. Chem. Phys. 2000, 113, 6042.
29. H. Fukunishi, O. Watanabe, S. Takada, J. Chem. Phys. 2002, 116, 9058.
30. S. Park, W. Im, J. Chem. Theory. Comput. 2013, 9, 13.
31. S. J. Fleishman, N. Ben-Tal, J. Mol. Biol. 2002, 321, 363.
32. K. S. Mineev, E. V. Bocharov, P. E. Volynsky, M. V. Goncharuk, E. N. Tkach, Y. S. Ermolyuk, A. A. Schulga, V. V. Chupin, I. V. Maslennikov, R. G. Efremov, R. G. Arseniev, Acta Naturae 2011, 3, 90.
33. E. V. Bocharov, M. L. Mayzel, P. E. Volynsky, M. V. Goncharuk, Y. S. Ermolyuk, A. A. Schulga, E. O. Artemenko, R. G. Efremov, A. S. Arseniev, J. Biol. Chem. 2008, 283, 29385.
34. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, J. M. Rosenberg, J. Comput. Chem. 1992, 13, 1011.
35. B. R. Brooks, C. L. Brooks, A. D. Mackerell, L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus, J. Comput. Chem. 2009, 30, 1545.
36. M. Feig, J. Karanicolas, C. L. Brooks, III, J. Mol. Graph. Model. 2004, 22, 377.
37. T. Lazaridis, M. Karplus, Proteins: Struct. Funct. Bioinf. 1999, 35, 133.
38. T. Lazaridis, Proteins: Struct. Funct. Genet. 2003, 52, 176.
39. W.E. Reiher, III, PhD Thesis, Department of Chemistry, Harvard University: Cambridge, MA, 1985.
40. E. Neria, S. Fischer, M. Karplus, J. Chem. Phys. 1996, 105, 1902.
41. A. D. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus, J. Phys. Chem. B 1998, 102, 3586.
42. A. D. Mackerell, M. Feig, C. L. Brooks, J. Comput. Chem. 2004, 25, 1400.
43. S. Chandrasekhar, Rev. Mod. Phys. 1943, 15, 0001.
44. A. Brunger, C. L. Brooks, M. Karplus, Chem. Phys. Lett. 1984, 105, 495.
45. J.-P. Ryckaert, G. Ciccotti, H. J. C. Berendsen, J. Comput. Phys. 1977, 23, 327.
46. W. P. Russ, D. M. Engelman, J. Mol. Biol. 2000, 296, 911.
47. A. Senes, M. Gerstein, D. M. Engelman, J. Mol. Biol. 2000, 296, 921.
48. L.-M. Munter, P. Voigt, A. Harmeier, D. Kaden, K. E. Gottschalk, C. Weise, R. Pipkorn, M. Schaefer, D. Langosch, G. Multhaup, EMBO J. 2007, 26, 1702.
49. E. V. Bocharov, M. L. Mayzel, P. E. Volynsky, K. S. Mineev, E. N. Tkach, Y. S. Ermolyuk, A. A. Schulga, R. G. Efremov, A. S. Arseniev, Biophys. J. 2010, 98 881.
50. O. Yuzlenko, T. Lazaridis, J. Comput. Chem. 2013, 34, 731.
51. N. Go, Annu. Rev. Biophys. Bioeng. 1983, 12, 183.
52. J. N. Onuchic, Z. Luthey-Schulten, P. G. Wolynes, Annu. Rev. Phys. Chem. 1997, 48, 545.
53. G. Bussi, F. L. Gervasio, A. Laio, M. Parrinello, J. Am. Chem. Soc. 2006, 128, 13435.
54. J. Hsin, C. Chipot, K. Schulten, J. Am. Chem. Soc. 2009, 131, 17096.
55. A. Arkhipov, Y. Shan, R. Das, N. F. Endres, M. P. Eastwood, D. E. Wemmer, J. Kuriyan, D. E. Shaw, Cell 2013, 152, 557.
56. X. Periole, A. M. Knepp, T. P. Sakmar, S. J. Marrink, T. J Huber, J. Am. Chem. Soc. 2012, 134, 10959.