Identification of slow molecular order parameters for Markov model construction

Journal of Chemical Physics

Volumn 139, Issue 1, 2013, Pages

  Pérez Hernández, Guillermo ^a   Paul, Fabian ^a,b   Giorgino, Toni ^c   De Fabritiis, Gianni ^d   Noé, Frank ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b MAX PLANCK INSTITUTE OF COLLOIDS AND INTERFACES   (Germany)

^c CNR   (Italy)

^d Barcelona Biomedical Research Park   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL DYNAMICS; EIGENVECTORS AND EIGENVALUES; INDEPENDENT COMPONENTS; KINETIC CHARACTERIZATION; MACROMOLECULAR SYSTEMS; MOLECULAR DYNAMICS SIMULATIONS; VARIATIONAL FORMULATION; VARIATIONAL PRINCIPLES;

EIGENVALUES AND EIGENFUNCTIONS; INDEPENDENT COMPONENT ANALYSIS; KINETICS; MARKOV PROCESSES; MOLECULAR DYNAMICS; OPTIMIZATION; RELAXATION PROCESSES; VARIATIONAL TECHNIQUES;

IDENTIFICATION (CONTROL SYSTEMS);

PHOSPHOTRANSFERASE;

ALGORITHM; CHEMISTRY; CONFORMATION; KINETICS; MOLECULAR DYNAMICS; PROBABILITY; PROTEIN TERTIARY STRUCTURE; TEMPERATURE; ARTICLE;

ALGORITHMS; KINETICS; MARKOV CHAINS; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; PHOSPHOTRANSFERASES; PROTEIN STRUCTURE, TERTIARY; TEMPERATURE;

EID: 84886081379     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4811489     Document Type: Article

References (86)

1. A. Gansen, A. Valeri, F. Hauger, S. Felekyan, S. Kalinin, K. Tóth, J. Langowski, and C. A. M. Seidel, Proc. Natl. Acad. Sci. U.S.A. 106, 15308 (2009).
2. H. Neubauer, N. Gaiko, S. Berger, J. Schaffer, C. Eggeling, J. Tuma, L. Verdier, C. A. Seidel, C. Griesinger, and A. Volkmer, J. Am. Chem. Soc. 129, 12746 (2007).
3. W. Min, G. Luo, B. J. Cherayil, S. C. Kou, and X. S. Xie, Phys. Rev. Lett. 94, 198302 (2005).
4. E. Z. Eisenmesser, O. Millet, W. Labeikovsky, D. M. Korzhnev, M. Wolf-Watz, D. A. Bosco, J. J. Skalicky, L. E. Kay, and D. Kern, Nature (London) 438, 117 (2005).
5. Y. Santoso, C. M. Joyce, O. Potapova, L. Le Reste, J. Hohlbein, J. P. Torella, N. D. F. Grindley, and A. N. Kapanidis, Proc. Natl. Acad. Sci. U.S.A. 107, 715 (2010).
6. J. C. M. Gebhardt, T. Bornschlögl, and M. Rief, Proc. Natl. Acad. Sci. U.S.A. 107, 2013 (2010).
7. B. G. Wensley, S. Batey, F. A. C. Bone, Z. M. Chan, N. R. Tumelty, A. Steward, L. G. Kwa, A. Borgia, and J. Clarke, Nature (London) 463, 685 (2010).
8. M. Jäger, Y. Zhang, J. Bieschke, H. Nguyen, M. Dendle, M. E. Bowman, J. P. Noel, M. Gruebele, and J. W. Kelly, Proc. Natl. Acad. Sci. U.S.A. 103, 10648 (2006).
9. A. Y. Kobitski, A. Nierth, M. Helm, A. Jäschke, and G. U. Nienhaus, Nucleic Acids Res. 35, 2047 (2007).
10. S. Fischer, B. Windshuegel, D. Horak, K. C. Holmes, and J. C. Smith, Proc. Natl. Acad. Sci. U.S.A. 102, 6873 (2005).
11. F. Noé, D. Krachtus, J. C. Smith, and S. Fischer, J. Chem. Theory Comput. 2, 840 (2006).
12. A. Ostermann, R. Waschipky, F. G. Parak, and U. G. Nienhaus, Nature (London) 404, 205 (2000).
13. M. Pirchi, G. Ziv, I. Riven, S. S. Cohen, N. Zohar, Y. Barak, and G. Haran, Nat. Commun. 2, 493 (2011).
14. J. Stigler, F. Ziegler, A. Gieseke, J. C. M. Gebhardt, and M. Rief, Science 334, 512 (2011).
15. H. Chung, J. Louis, and W. Eaton, Science 335, 981 (2012).
16. 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).
17. K. Lindorff-Larsen, S. Piana, R. O. Dror, and D. E. Shaw, Science 334, 517 (2011).
18. V. A. Voelz, G. R. Bowman, K. Beauchamp, and V. S. Pande, J. Am. Chem. Soc. 132, 1526 (2010).
19. G. R. Bowman, V. A. Voelz, and V. S. Pande, J. Am. Chem. Soc. 133, 664 (2011).
20. F. Noé, C. Schütte, E. Vanden-Eijnden, L. Reich, and T. R. Weikl, Proc. Natl. Acad. Sci. U.S.A. 106, 19011 (2009).
21. I. Buch, T. Giorgino, and G. De Fabritiis, Proc. Natl. Acad. Sci. U.S.A. 108, 10184 (2011).
22. S. K. Sadiq, F. Noé, and G. De Fabritiis, Proc. Natl. Acad. Sci. U.S.A. 109, 20449 (2012).
23. I. Buch, M. J. Harvey, T. Giorgino, D. P. Anderson, and G. De Fabritiis, J. Chem. Inf. Model. 50, 397 (2010).
24. D. J. Wales, Energy Landscapes (Cambridge University Press, Cambridge, 2003).
25. F. Noé and S. Fischer, Curr. Opin. Struct. Biol. 18, 154 (2008).
26. M. E. Karpen, D. J. Tobias, and C. L. Brooks, Biochemistry 32, 412 (1993).
27. I. A. Hubner, E. J. Deeds, and E. I. Shakhnovich, Proc. Natl. Acad. Sci. U.S.A. 103, 17747 (2006).
28. M. Weber, ZIB Report No. 03-04, 2003.
29. N. V. Buchete and G. Hummer, J. Phys. Chem. B 112, 6057 (2008).
30. F. Rao and A. Caflisch, J. Mol. Biol. 342, 299 (2004).
31. S. Muff and A. Caflisch, Proteins 70, 1185 (2007).
32. B. de Groot, X. Daura, A. Mark, and H. Grubmüller, J. Mol. Biol. 309, 299 (2001).
33. V. Schultheis, T. Hirschberger, H. Carstens, and P. Tavan, J. Chem. Theory Comput. 1, 515 (2005).
34. A. C. Pan and B. Roux, J. Chem. Phys. 129, 064107 (2008).
35. S. V. Krivov and M. Karplus, Proc. Natl. Acad. Sci. U.S.A. 101, 14766 (2004).
36. F. Noé, I. Horenko, C. Schütte, and J. C. Smith, J. Chem. Phys. 126, 155102 (2007).
37. J. D. Chodera, K. A. Dill, N. Singhal, V. S. Pande, W. C. Swope, and J. W. Pitera, J. Chem. Phys. 126, 155101 (2007).
38. W. C. Swope, J. W. Pitera, and F. Suits, J. Phys. Chem. B 108, 6571 (2004).
39. D. Huang and A. Caflisch, PLOS Comput. Biol. 7, e1002002 (2011).
40. R. R. Coifman, S. Lafon, A. B. Lee, M. Maggioni, B. Nadler, F. Warner, and S. W. Zucker, Proc. Natl. Acad. Sci. U.S.A. 102, 7426 (2005).
41. M. A. Rohrdanz, W. Zheng, M. Maggioni, and C. Clementi, J. Chem. Phys. 134, 124116 (2011).
42. S. Sriraman, I. G. Kevrekidis, and G. Hummer, J. Phys. Chem. B 109, 6479 (2005).
43. F. Noé, J. Chem. Phys. 128, 244103 (2008).
44. N. Singhal and V. S. Pande, J. Chem. Phys. 123, 204909 (2005).
45. M. Sarich, F. Noé, and C. Schütte, Multiscale Model. Simul. 8, 1154 (2010).
46. C. Schütte, A. Fischer, W. Huisinga, and P. Deuflhard, J. Comput. Phys. 151, 146 (1999).
47. F. Noé and F. Nüske, "A variational approach to modeling slow processes in stochastic dynamical systems," Multiscale Model. Simul. (in press), http://arxiv.org/abs/1211.7103v1.
48. P. Deuflhard and M. Weber, ZIB Report No. 03-09, 2003.
49. J.-H. Prinz, H. Wu, M. Sarich, B. Keller, M. Fischbach, M. Held, J. D. Chodera, C. Schütte, and F. Noé, J. Chem. Phys. 134, 174105 (2011).
50. F. Noé, S. Doose, I. Daidone, M. Löllmann, J. D. Chodera, M. Sauer, and J. C. Smith, Proc. Natl. Acad. Sci. U.S.A. 108, 4822 (2011).
51. B. Keller, J.-H. Prinz, and F. Noé, Chem. Phys. 396, 92 (2012).
52. G. S. Buchner, R. D. Murphy, N.-V. Buchete, and J. Kubelka, Biochim. Biophys. Acta 1814, 1001 (2011).
53. S. Kube and M. Weber, J. Chem. Phys. 126, 024103 (2007).
54. P. Metzner, C. Schütte, and E. V. Eijnden, Multiscale Model. Simul. 7, 1192 (2009).
55. A. Berezhkovskii, G. Hummer, and A. Szabo, J. Chem. Phys. 130, 205102 (2009).
56. N. Djurdjevac, M. Sarich, and C. Schütte, Multiscale Model. Simul. 10, 61 (2012).
57. J.-H. Prinz, J. D. Chodera, and F. Noé, "Spectral rate theory for two-state kinetics," Phys. Rev. (submitted).
58. G. Berezovska, D. Prada-Gracia, S. Mostarda, and F. Rao, J. Chem. Phys. 137, 194101 (2012).
59. W. Kabsch, Acta Crystallogr., Sect. A: Cryst. Phys., Diffr., Theor. Gen. Crystallogr. 32, 922 (1976).
60. G. R. Bowman, K. A. Beauchamp, G. Boxer, and V. S. Pande, J. Chem. Phys. 131, 124101 (2009).
61. K. A. Beauchamp, R. McGibbon, Y.-S. Lin, and V. S. Pande, Proc. Natl. Acad. Sci. U.S.A. 109, 17807 (2012).
62. G. R. Bowman and P. L. Geissler, Proc. Natl. Acad. Sci. U.S.A. 109, 11681 (2012).
63. A. Amadei, A. B. Linssen, and H. J. C. Berendsen, Proteins 17, 412 (1993).
64. L. Molgedey and H. G. Schuster, Phys. Rev. Lett. 72, 3634 (1994).
65. A. Hyvärinen, J. Karhunen, and E. Oja, Independent Component Analysis (John Wiley & Sons, 2001) Chap. 18, p. 344.
66. Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011).
67. A. Mitsutake, H. Iijima, and H. Takano, J. Chem. Phys. 135, 164102 (2011).
68. C. R. Schwantes and V. S. Pande, J. Chem. Theory Comput. 9, 2000 (2013).
69. W. Ritz, J. Reine Angew. Math. 135, 1 (1909).
70. See supplementary material at http://dx.doi.org/10.1063/1.4811489 for the mathematical derivation of TICA using variational calculus, the sym-metrization of the time-lagged covariance matrix, the simulation setup for KID, and statistical uncertainties in the estimated implied timescales.
71. L. Tong, V. C. Soon, Y. F. Huang, and R. Liu, Circuits Syst. 3, 1784 (1990).
72. M. Senne, B. Trendelkamp-Schroer, A. Mey, C. Schütte, and F. Noé, J. Chem. Theory Comput. 8, 2223 (2012).
73. K. A. Beauchamp, G. R. Bowman, T. J. Lane, L. Maibaum, I. S. Haque, and V. S. Pande, J. Chem. Theory Comput. 7, 3412 (2011).
74. M. Seeber, A. Felline, F. Raimondi, S. Muff, R. Friedman, F. Rao, A. Caflisch, and F. Fanelli, J. Comput. Chem. 32, 1183 (2011).
75. X. Biarnés, F. Pietrucci, F. Marinelli, and A. Laio, Comput. Phys. Commun. 183, 203 (2012).
76. S. Lloyd, IEEE Trans. Inf. Theory 28, 129 (1982).
77. H. Neuweiler, M. Löllmann, S. Doose, and M. Sauer, J. Mol. Biol. 365, 856 (2007).
78. I. Daidone, H. Neuweiler, S. Doose, M. Sauer, and J. C. Smith, PLOS Comput. Biol. 6, e1000645 (2010).
79. F. Noé, I. Daidone, J. C. Smith, A. di Nola, and A. Amadei, J. Phys. Chem. B 112, 11155 (2008).
80. L. H. Kasper, T. Fukuyama, M. A. Biesen, F. Boussouar, C. Tong, A. de Pauw, P. J. Murray, J. M. A. van Deursen, and P. K. Brindle, Mol. Cell. Biol. 26, 789 (2006).
81. V. N. Uversky, Int. J. Biochem. Cell Biol. 43, 1090 (2011).
82. K. Sugase, H. J. Dyson, and P. E. Wright, Nature (London) 447, 1021 (2007).
83. A. Mohan, C. J. Oldfield, P. Radivojac, V. Vacic, M. S. Cortese, A. K. Dunker, and V. N. Uversky, J. Mol. Biol. 362, 1043 (2006).
84. B. A. Shoemaker, J. J. Portman, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. 97, 8868 (2000).
85. M. J. Harvey, G. Giupponi, and G. D. Fabritiis, J. Chem. Theory Comput. 5, 1632 (2009).
86. I. Radhakrishnan, G. C. Pérez-Alvarado, D. Parker, H. Dyson, M. R. Montminy, and P. E. Wright, Cell 91, 741 (1997).