A novel computer simulation method for simulating the multiscale transduction dynamics of signal proteins

Journal of Chemical Physics

Volumn 136, Issue 12, 2012, Pages

  Peter, Emanuel ^a   Dick, Bernhard ^a   Baeurle, Stephan A ^a  

^a UNIVERSITY OF REGENSBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMISTIC RESOLUTION; AVENA SATIVA; CANCER CELLS; CELLULAR PROCESS; COMPLEX SIGNAL; COMPUTATIONAL COSTS; LIGHT STIMULI; LIVING SYSTEMS; MONTE CARLO; MULTISCALES; PROTEIN SYSTEM; RE-ARRANGEMENT; SIGNAL ACTIVATION; SIGNALING PATHWAYS; SIGNALING PROCESS; TIME-SCALES;

AMINO ACIDS; BACTERIOPHAGES; BIOCHEMISTRY; CHROMOPHORES; COMPUTER SIMULATION; DYNAMICS; PIGMENTS; PROTEINS; SIGNALING;

SIGNAL TRANSDUCTION;

PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; COMPUTER SIMULATION; HUMAN; MOLECULAR DYNAMICS; OAT; PROTEIN CONFORMATION; SIGNAL TRANSDUCTION; THEORETICAL MODEL;

ALGORITHMS; AVENA SATIVA; COMPUTER SIMULATION; HUMANS; MODELS, THEORETICAL; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEINS; SIGNAL TRANSDUCTION;

EID: 84859550742     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3697370     Document Type: Article

References (78)

1. J. B. Pereira-Leal, E. D. Levy, and S. A. Teichmann, Philos. Trans. R. Soc. London Ser. B 361, 507 (2006). 10.1098/rstb.2005.1807 (Pubitemid 44870107)
2. K. Wennerberg and C. J. Der, J. Cell Sci. 117, 1301 (2004). 10.1242/jcs.01118 (Pubitemid 38559808)
3. A. Singh, A. E. Karnoub, T. R. Palmby, E. Lengyel, J. Sondek, and C. J. Der, Oncogene 23, 9369 (2004). 10.1038/sj.onc.1208182 (Pubitemid 40069669)
4. P. Hegemann, Annu. Rev. Plant. Biol. 59, 167 (2008). 10.1146/annurev. arplant.59.032607.092847 (Pubitemid 351813028)
5. J. M. Christie, Annu. Rev. Plant. Biol. 58, 21 (2007). 10.1146/annurev.arplant.58.032806.103951 (Pubitemid 46986316)
6. W. R. Briggs, J. Biomed. Sci. 14, 499 (2007). 10.1007/s11373-007-9162-6 (Pubitemid 47063482)
7. T. Kottke, P. Hegemann, B. Dick, and J. Heberle, Biopolymers 82, 373 (2006). 10.1002/bip.20510
8. M. A. Jones, K. A. Feeney, S. M. Kelly, and J. M. Christie, J. Biol. Chem. 282, 6405 (2007). 10.1074/jbc.M605969200 (Pubitemid 47100883)
9. D. Matsuoka and S. Tokutomi, Proc. Natl. Acad. Sci. U.S.A. 102, 13337 (2005). 10.1073/pnas.0506402102 (Pubitemid 41325024)
10. A. S. Halavaty and K. Moffat, Biochemistry 46, 14001 (2007). 10.1021/bi701543e (Pubitemid 350250297)
11. S. M. Harper, L. C. Neil, and K. H. Gardner, Science 301, 1541 (2003). 10.1126/science.1086810 (Pubitemid 37128547)
12. S. M. Harper, J. M. Christie, and K. H. Gardner, Biochemistry 43, 16184 (2004). 10.1021/bi048092i (Pubitemid 40041031)
13. S. Crosson and K. Moffat, Plant Cell 14, 1067 (2002). 10.1105/tpc.010475 (Pubitemid 34609217)
14. E. Peter, B. Dick, and S. A. Baeurle, Nat. Commun. 1, 122 (2010). 10.1038/ncomms1121
15. Y. I. Wu, D. Frey, O. I. Lungu, A. Jaehrig, I. Schlichting, B. Kuhlman, and K. M. Hahn, Nature (London) 461, 104 (2009). 10.1038/nature08241
16. E. Peter, B. Dick, and S. A. Baeurle, Proteins: Struct., Funct., Bioinf. (2012).
17. M. Karplus and J. Kuriyan, Proc. Natl. Acad. Sci. U.S.A. 102, 6679 (2005), and references therein. 10.1073/pnas.0408930102 (Pubitemid 40675376)
18. S. A. Baeurle, J. Math. Chem. 46, 363 (2009). 10.1007/s10910-008-9467-3
19. Y. Nakasone, T. Eitoku, D. Matsuoka, S. Tokutomi, and M. Terazima, J. Mol. Biol. 367, 432 (2007). 10.1016/j.jmb.2006.12.074 (Pubitemid 46295433)
20. W. R. P. Scott, P. H. Hunenberger, I. G. Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Kruger, and W. F. van Gunsteren, J. Phys. Chem. A 103, 3596 (1999). 10.1021/jp984217f
21. L. Monticelli, S. K. Kandasamy, X. Periole, R. G. Larson, D. P. Tieleman, and S. J. Marrink, J. Chem. Theory Comput. 4, 819 (2008). 10.1021/ct700324x
22. A. J. Rzepiela, L. V. Schäfer, N. Goga, H. J. Risselada, A. de Vries, and S. J. Marrink, J. Comput. Chem. 31, 1333 (2010). 10.1002/jcc.21415
23. H. M. Senn and W. Thiel, Top Curr. Chem. 268, 173 (2007). 10.1007/978-3-540-38085-6
24. J. Noolandi, T. S. Davison, A. R. Völkel, X.-F. Nie, C. Kay, and C. H. Arrowsmith, Proc. Natl. Acad. Sci. U.S.A. 97, 9955 (2000). 10.1073/pnas.160075697
25. A. R. Völkel and J. Noolandi, Biophys. J. 80, 1524 (2001). 10.1016/S0006-3495(01)76125-5
26. T. Coussaert, A. R. Völkel, J. Noolandi and A. P. Gast, Biophys. J. 80, 2004 (2001). 10.1016/S0006-3495(01)76170-X
27. G. S. Ayton and G. A. Voth, Curr. Opin. Struct. Biol. 19, 138 (2009), and references therein. 10.1016/j.sbi.2009.03.001
28. M. Tuckerman, B. J. Berne, and G. J. Martyna, J. Chem. Phys. 97, 1990 (1992). 10.1063/1.463137
29. C. R. Sweet, P. Petrone, V. S. Pande, and J. A. Izaguirre, J. Chem. Phys. 128, 145101 (2008). 10.1063/1.2883966 (Pubitemid 351551818)
30. J. A. Izaguirre, C. R. Sweet, and V. S. Pande, Pac. Symp. Biocomput. 15, 240 (2010).
31. 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. Shan, and W. Wriggers, Science 330, 341 (2010). 10.1126/science.1187409
32. V. A. Voelz, G. R. Bowman, K. Beauchamp, and V. S. Pande, J. Am. Chem. Soc. 132, 1526 (2010). 10.1021/ja9090353
33. M. Shirts and V. S. Pande, Science 290, 1903 (2000). 10.1126/science.290. 5498.1903
34. D. E. Shaw, R. O. Dror, J. K. Salmon, J. P. Grossman, K. M. Mackenzie, J. A. Bank, C. Young, M. M. Deneroff, B. Batson, K. J. Bowers, E. Chow, M. P. Eastwood, D. J. Ierardi, J. L. Klepeis, J. S. Kuskin, R. H. Larson, K. Lindorff-Larsen, P. Maragakis, M. A. Moraes, S. Piana, Y. Shan, and B. Towles, in Proceedings of the Conference on High Performance Computing, Networking, Storage and Analysis (SC09) (ACM, New York, 2009), pp. 1-11.
35. J. A. Izaguirre and S. S. Hampton, J. Comput. Phys. 200, 581 (2004). 10.1016/j.jcp.2004.04.016
36. H. Grubmueller, Phys. Rev. E 52, 2893 (1995). 10.1103/PhysRevE.52.2893
37. A. Barducci, R. Chelli, P. Procacci, V. Schettino, F. L. Gervasio, and M. Parrinello, J. Am. Chem. Soc. 128, 2705 (2006). 10.1021/ja057076l (Pubitemid 43328887)
38. A. B. Bortz, M. H. Kalos, and J. L. Lebowitz, J. Comput. Phys. 17, 10 (1975). 10.1016/0021-9991(75)90060-1
39. D. E. Makarov and H. Metiu, J. Chem. Phys. 116, 5205 (2002). 10.1063/1.1450123 (Pubitemid 34923876)
40. D. E. Makarov, C. A. Keller, K. W. Plaxco, and H. Metiu, Proc. Natl. Acad. Sci. U.S.A. 99, 3535 (2002). 10.1073/pnas.052713599 (Pubitemid 34252143)
41. O. Collet, Phys. Rev. E 67, 061912 (2003). 10.1103/PhysRevE.67.061912
42. D. E. Makarov, P. K. Hansma, and H. Metiu, J. Chem. Phys. 114, 9663 (2001). 10.1063/1.1369622 (Pubitemid 32535635)
43. P.-C. Li and D. E. Makarov, J. Chem. Phys. 119, 9260 (2003). 10.1063/1.1615233
44. M. Rief, M. Gautel, F. Oesterhelt, J. M. Fernandez, and H. E. Gaub, Science 276, 1109 (1997). 10.1126/science.276.5315.1109 (Pubitemid 27218118)
45. A. F. Voter, Introduction to the kinetic Monte Carlo method., in Radiation Effects in Solids, edited by, K. E. Sickafus, E. A. Kotomin, and, B. P. Uberuaga, (Springer, Berlin, 2007), Vol. 235, pp. 1-23.
46. J. Howard, Mechanics of motor proteins., in Physics of Bio-Molecules and Cells, 75th Les Houches Summer School, edited by, H. Flyvbjerg, F. Jülicher, P. Ormos, and, F. David, (Springer-Verlag, Berlin, 2002), Vol. 75, pp. 69-94.
47. A. A. Gurtovenko and Y. Y. Gotlib, J. Chem. Phys. 115, 6785 (2001). 10.1063/1.1401819 (Pubitemid 33046654)
48. V. B. P. Leite, J. N. Onuchic, G. Stell, and J. Wang, Biophys. J. 87, 3633 (2004). 10.1529/biophysj.104.046243 (Pubitemid 39602874)
49. P. L. Freddolino, M. Dittrich, and K. Schulten, Biophys. J. 91, 3630 (2006). 10.1529/biophysj.106.088609 (Pubitemid 44788306)
50. T. Kottke, J. Heberle, D. Hehn, B. Dick, and P. Hegemann, Biophys. J. 84, 1192 (2003). 10.1016/S0006-3495(03)74933-9
51. R. Fedorov, I. Schlichting, E. Hartmann, T. Domratcheva, M. Fuhrmann, and P. Hegemann, Biophys. J. 84, 2474 (2003). 10.1016/S0006-3495(03)75052-8
52. E. Peter, B. Dick, and S. A. Baeurle, Signals of LOV1: a computer simulation study on the wildtype LOV1-domain of Chlamydomonas reinhardtii and its mutants., J. Mol. Model. (to be published). 10.1007/s00894-011-1165-6
53. E. Peter, B. Dick, and S. A. Baeurle, J. Chem. Biol. 4, 167 (2011). 10.1007/s12154-011-0060-z
54. E. Peter, B. Dick, and S. A. Baeurle, Proteins: Struct., Funct., Bioinf. 80, 471 (2012). 10.1002/prot.23213
55. K. J. Laidler and M. C. King, J. Phys. Chem. 87, 2657 (1983). 10.1021/j100238a002
56. D. K. Roylance, Characterization of polymer deformation and fracture., in Applications of Polymer Spectroscopy, edited by, E. G. Brame, (Academic, New York, 1978), pp. 207-219.
57. T. Keii, Heterogeneous Kinetics: Theory of Ziegler-Natta-Kaminsky Polymerization (Springer Series in Chemical Physics, Berlin, 2004), pp. 59-60.
58. D. C. Liu and J. Nocedal, Math. Program 45, 503 (1989). 10.1007/BF01589116
59. D. Fincham, N. Quirke, and D. J. Tildesley, J. Chem. Phys. 84, 4535 (1986). 10.1063/1.450824
60. See supplementary material at http://dx.doi.org/10.1063/1.3697370 E-JCPSA6-136-014213 for the process pathes of the H-bond breakage, H-bond formation as well as side chain rotation events. In addition detailed information is provided about the determination of the pre-exponential factors for the KMC-MD simulations of the AsLOV2-J- and PA-Rac1-systems.
61. A. Luzar and D. Chandler, J. Chem. Phys. 98, 8160 (1993). 10.1063/1.464521
62. B. Hetenyi, F. De Angelis, P. Giannozzi, and R. Car, J. Chem. Phys. 120, 8632 (2004). 10.1063/1.1703526
63. I. W. Kuo and C. J. Mundy, Science 303, 658 (2004). 10.1126/science. 1092787 (Pubitemid 38141628)
64. Y. Zhang, M. Lagi, D. Liu, F. Mallamace, E. Fratini, P. Baglioni, E. Mamontov, M. Hagen, and S.-H. Chen, J. Chem. Phys. 130, 135101 (2009). 10.1063/1.3081137
65. E. Lindahl, B. Hess, and D. van der Spoel, J. Mol. Model. 7, 306 (2001).
66. T. Soares, X. Daura, C. Oostenbrink, L. Smith, and W. Gunsteren, J. Biomol. NMR 30, 407 (2004). 10.1007/s10858-004-5430-1 (Pubitemid 40069205)
67. N. Todorova, F. S. Legge, H. Treutlein, and I. Yarovsky, J. Phys. Chem. 112, 11137 (2008). 10.1021/jp076825d
68. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications (Academic, San Diego, 2003).
69. C. Neiss and P. Saalfrank, Photochem. Photobiol. 77, 101 (2003). 10.1562/0031-8655(2003)0770101:AIQCIO2.0.CO;2
70. A. I. Nash, W.-H. Ko, S. M. Harper, and K. H. Gardner, Biochemistry 47, 13842 (2008). 10.1021/bi801430e
71. M. T. A. Alexandre, R. van Grondelle, K. J. Hellingwerf, and J. T. M. Kennis, Biophys. J. 97, 238 (2009). 10.1016/j.bpj.2009.03.047
72. S. Arai, M. Togashi, M. Shiozawa, Y. Inoue, and M. Sakurai, Chem. Phys. Lett. 414, 230 (2005). 10.1016/j.cplett.2005.08.076 (Pubitemid 41764947)
73. A. Pfeifer, T. Majerus, K. Zikihara, D. Matsuoka, S. Tokutomi, J. Heberle, and T. Kottke, Biophys. J. 96, 1462 (2009). 10.1016/j.bpj.2008.11.016
74. C. DerMadirossian, A. Schnelzer, and G. M. Bokoch, Mol. Cell 15, 117 (2004). 10.1016/j.molcel.2004.05.019 (Pubitemid 38850224)
75. D. Owen, L. J. Campbell, K. Littlefield, K. A. Evetts, Z. Li, D. B. Sacks, P. N. Lowe, and H. R. Mott, J. Biol. Chem. 283, 1692 (2008). 10.1074/jbc.M707257200
76. J. Yamauchi, Y. Miyamoto, A. Sanbe, and A. Tanoue, Exp. Cell Res. 312, 2954 (2006). 10.1016/j.yexcr.2006.05.016
77. A. Deiters, ChemBioChem 11, 47 (2010). 10.1002/cbic.200900529
78. A. Deiters, Curr. Opin. Chem. Biol. 13, 678 (2009). 10.1016/j.cbpa.2009. 09.026