Multibody local approximation: Application to conformational entropy calculations on biomolecules

Journal of Chemical Physics

Volumn 137, Issue 8, 2012, Pages

  Suárez, Ernesto ^a   Suárez, Dimas ^b  

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

^b UNIVERSITY OF OVIEDO   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ENTROPY; MOLECULAR DYNAMICS; RIGID ROTORS;

COMBINATORIAL EXPLOSION; COMPUTATIONAL COSTS; CONFORMATIONAL ENTROPY; ENTROPIC CONTRIBUTIONS; HARMONIC OSCILLATORS; LOCAL APPROXIMATION; MOLECULAR DYNAMICS TRAJECTORIES; MUTUAL INFORMATIONS;

CONFORMATIONS;

PEPTIDE;

ARTICLE; CHEMISTRY; CONFORMATION; ENTROPY; MOLECULAR DYNAMICS;

ENTROPY; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; PEPTIDES;

EID: 84865736993     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4748104     Document Type: Article

References (40)

1. R. Drautz, M. Fähnle, and J. M. Sanchez, J. Phys.: Condens. Matter 16, 3843 (2004); 10.1088/0953-8984/16/23/005
2. V. Sundararaghavan and N. Zabaras, Phys. Rev. B 77, 064101 (2008). 10.1103/PhysRevB.77.064101
3. V. Hnizdo, J. Tan, B. J. Killian, and M. K. Gilson, J. Comput. Chem. 29, 1605 (2008). 10.1002/jcc.20919
4. H. Matsuda, Phys. Rev. E 62, 3098 (2000). 10.1103/PhysRevE.62.3096
5. K. Babu and S. R. Gadre, J. Comput. Chem. 24, 484 (2003). 10.1002/jcc.10206
6. See supplementary material at http://dx.doi.org/10.1063/1.4748104 E-JCPSA6-137-037233 for mathematical proofs (Propositions 1-4); strategy followed in the reordering of the elements of the system to minimize the number of the additional terms; Table S1 showing the dependence of SR(n) and its computational cost on the order and cutoff; a complementary discussion on the applicability of the classical MIE approach; and the discussion includes Figure S1 and Table S2 that show a poor order convergence of the MIE results for the fTHP-5 system.
7. B. J. Killian, J. Y. Kravitz, and M. K. Gilson, J. Chem. Phys. 127, 024107 (2007); 10.1063/1.2746329 (Pubitemid 47114637)
8. E. E. Dahlke and D. G. Truhlar, J. Phys. Chem. B 110, 10595 (2006). 10.1021/jp061039e (Pubitemid 43958677)
9. E. Suárez, N. Díaz, and D. Suárez, J. Chem. Theory Comput. 7 (8), 2638 (2011). 10.1021/ct200216n
10. E. Suárez, N. Díaz, and D. Suárez, J. Phys. Chem. B 112, 15248 (2008). 10.1021/jp8074699
11. C. A. Chang, C. Chen, and M. K. Gilson, Proc. Natl. Acad. Sci. U.S.A. 104, 1534 (2007); 10.1073/pnas.0610494104 (Pubitemid 46214625)
12. M. Karplus, T. Ichiye, and B. M. Pettit, Biophys. J. 52, 1083 (1987); 10.1016/S0006-3495(87)83303-9
13. H.-X. Zhou and M. K. Gilson, Chem. Rev. 109, 4092 (2009). 10.1021/cr800551w
14. I. Andricioaei and M. Karplus, J. Chem. Phys. 115 (14), 6289 (2001). 10.1063/1.1401821 (Pubitemid 33046603)
15. L. Comtet, Advanced Combinatorics: The Art of Finite and Infinite Expansions., (Reidel, Holland, 1974).
16. E. Suárez, N. Díaz, and D. Suárez, J. Chem. Theory Comput. 5, 1667 (2009). 10.1021/ct8005002
17. B. M. King, N. W. Silver, and B. Tidor, J. Phys. Chem. B 116, 2891-2904 (2012). 10.1021/jp2068123
18. S. S. Choa, Y. Levya, and P. G. Wolynesa, Proc. Natl. Acad. Sci. U.S.A. 106 (2), 434 (2009); 10.1073/pnas.0810218105
19. A. Bachmann, T. Kiefhaber, S. Boudko, J. Engel, and H. P. Bächinger, Proc. Natl. Acad. Sci. U.S.A. 102 (39), 13897 (2005); 10.1073/pnas.0505141102 (Pubitemid 41377675)
20. C. Diehl, S. Genheden, K. Modig, U. Ryde, and M. Akke, J. Biomol. NMR 45, 157 (2009). 10.1007/s10858-009-9356-5
21. A. Kraskov, H. Stögbauer, R. G. Andrzejak, and P. Grassberger, Europhys. Lett. 70 (2), 278 (2005). 10.1209/epl/i2004-10483-y (Pubitemid 40551301)
22. J. L. Lauer-Fields, K. A. Tuzinski, K.-I. Shimokawa, H. Nagase, and G. B. Fields, J. Biol. Chem. 275, 13282 (2000); 10.1074/jbc.275.18.13282 (Pubitemid 30257384)
23. J. L. Lauer-Fields, P. Kele, G. Sui, H. Nagase, R. M. Leblanc, and G. B. Fields, Anal. Biochem. 321, 105 (2003). 10.1016/S0003-2697(03)00460-3 (Pubitemid 37086688)
24. L. Paninski, Neural Comput. 15 (6), 1191 (2003). 10.1162/ 089976603321780272 (Pubitemid 37049793)
25. G. Miller, in Information Theory in Psychology: Problems and Methods, edited by, H. Quastler, (The Free Press, 1955), p. 95.
26. D. Holste, I. Groe, and H. Herzel, J. Phys. A 31, 2551 (1998); 10.1088/0305-4470/31/11/007 (Pubitemid 128042654)
27. T. Schürmann and P. Grassberger, Chaos 6, 414 (1996). 10.1063/1.166191 (Pubitemid 126130993)
28. A. Chao and T.-J. Shen, Environ. Ecol. Stat. 10, 429 (2003). 10.1023/A:1026096204727 (Pubitemid 37450541)
29. H. L. Finke, J. Am. Chem. Soc. 76, 333 (1954). 10.1021/ja01631a005
30. R. A. Brown and D. A. Case, J. Comput. Chem. 27, 1662 (2006). 10.1002/jcc.20479 (Pubitemid 44476663)
31. C. Chang, W. Chen, and M. K. Gilson, J. Chem. Theory Comput. 1 (5), 1017 (2005); 10.1021/ct0500904
32. R. Baron, W. F. v. Gunsteren, and P. H. Hünenberger, Trends Phys. Chem. 11, 88 (2006).
33. Y. Duan, C. Wu, S. Chowdhury, M. C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. Wang, and P. Kollman, J. Comput. Chem. 14, 1999 (2003). 10.1002/jcc.10349
34. J. Tomasi, B. Mennucci, and E. Cancès, J. Mol. Struct.: THEOCHEM 464 (1-3), 211 (1999). 10.1016/S0166-1280(98)00553-3
35. M. J. Frisch, G. W. Trucks, H. B. Schlegel, GAUSSIAN 03, Revision A.1, Gaussian, Inc., Pittsburgh, PA, 2003.
36. C. I. Bayly, P. Cieplak, W. Cornell, and P. A. Kollman, J. Phys. Chem. 97 (40), 10269 (1993). 10.1021/j100142a004
37. D. A. Case, T. A. Darden, T. E. Cheatham, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, M. Crowley, R. C. Walker, W. Zhang, K. M. Merz, B. Wang, S. Hayik, A. Roitberg, G. Seabra, K. F. Kolossvary, K. F. Wong, F. Paesani, J. Vanicek, X. Wu, S. Brozell, T. Steinbrecher, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D. H. Mathews, M. G. Seetin, C. Sagui, V. Babin, and P. A. Kollman, AMBER 10, University of California, San Francisco, 2008;
38. I. Kolossváry and W. C. Guida, J. Am. Chem. Soc. 118, 5011 (1996). 10.1021/ja952478m (Pubitemid 26200976)
39. J. Srinivasan, T. E. Cheatham, P. Cieplak, P. A. Kollman, and D. A. Case, J. Am. Chem. Soc. 120 (37), 9401 (1998). 10.1021/ja981844+ (Pubitemid 28452628)
40. T. Macke and D. A. Case, Modeling Unusual Nucleic Acid Structures (American Chemical Society, Washington, DC, 1998).