Discovering free energy basins for macromolecular systems via guided multiscale simulation

Journal of Physical Chemistry B

Volumn 116, Issue 29, 2012, Pages 8534-8544

  Sereda, Yuriy V ^a   Singharoy, Abhishek B ^a   Jarrold, Martin F ^a   Ortoleva, Peter J ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC FORCE MICROSCOPY; ELECTRON ENERGY LEVELS; MACROMOLECULES; MASS SPECTROMETRY; MOLECULAR DYNAMICS;

AUTOMATED DISCOVERY; CHEMICAL LABELING; COARSE-GRAINED VARIABLES; ENERGY BASINS; ENERGY MINIMA; ENERGY MINIMIZING; ENTROPY CHANGES; FREE ENERGY LANDSCAPE; ION MOBILITY-MASS SPECTROMETRY; LACTOFERRIN; LANGEVIN DYNAMICS; LARGE-SCALE STRUCTURE; MACROMOLECULAR SYSTEMS; MULTI-SCALE SIMULATION; NANO-CHARACTERIZATION;

FREE ENERGY;

EID: 84864212825     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp2126174     Document Type: Article

References (52)

1. Ruotolo, B. T.; Giles, K.; Campuzano, I.; Sandercock, A. M.; Bateman, R. H.; Robinson, C. V. Science 2005, 310, 1658-1661
2. Binnig, G.; Quate, C. F.; Gerber, C. Phys. Rev. Lett. 1986, 56, 930
3. Beardsley, R. L.; Running, W. E.; Reilly, J. P. J. Proteome Res. 2006, 5, 2935-2946
4. Keyser, U. F.; Koeleman, B. N.; van Dorp, S.; Krapf, D.; Smeets, R. M. M.; Lemay, S. G.; Dekker, N. H.; Dekker, C. Nat. Phys. 2006, 2, 473-477
5. Joshi, H.; Singharoy, A. B.; Sereda, Y. V.; Cheluvaraja, S. C.; Ortoleva, P. J. Prog. Biophys. Mol. Biol. 2011, 107, 200-217
6. Rangwala, H.; Karypis, G. Introduction to Protein Structure Prediction. In Introduction to Protein Structure Prediction; John Wiley & Sons, Inc.: New York, 2010; pp 1-13.
7. Desmet, J.; Maeyer, M. D.; Hazes, B.; Lasters, I. Nature 1992, 356, 539-542
8. Georgiev, I.; Donald, B. R. Bioinformatics 2007, 23, i185-i194
9. Heath, A. P.; Kavraki, L. E.; Clementi, C. Proteins: Struct., Funct., Bioinf. 2007, 68, 646-661
10. Bower, M.; Cohen, F.; Dunbrack, R. J. Mol. Biol. 1997, 267, 1268-1282
11. Lee, C.; Subbiah, S. J. Mol. Biol. 1991, 217, 373-388
12. Lee, C. J. Mol. Biol. 1994, 236, 918-939
13. Floudas, C. A. Biotechnol. Bioeng. 2007, 97, 207-213
14. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J. Chem. Phys. 1953, 21, 1087-1092
15. Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P. Science 1983, 220, 671-680
16. Lee, C.; Levitt, M. Nature 1991, 352, 448-451
17. Holland, J. H. Adaptation in natural and artificial systems; The University of Michigan Press: Ann Harbor, MI, 1975.
18. Unger, R. The Genetic Algorithm Approach to Protein Structure Prediction. In Applications of Evolutionary Computation in Chemistry; Johnston, R. L., Ed.; Springer: Berlin/Heidelberg, 2004; Vol. 110, pp 2697-2699.
19. Kim, M. K.; Jernigan, R. L.; Chirikjian, G. S. Biophys. J. 2005, 89, 43-55
20. Marques, O.; Sanejouand, Y.-H. Proteins: Struct., Funct., Bioinf. 1995, 23, 557-560
21. Dellago, C.; Bolhuis, P. Transition Path Sampling and Other Advanced Simulation Techniques for Rare Events. In Advanced Computer Simulation Approaches for Soft Matter Sciences III; Holm, C.; Kremer, K., Eds.; Springer: Berlin/Heidelberg, 2009; Vol. 221, pp 167-233.
22. Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562-12566
23. Barducci, A.; Bonomi, M.; Parrinello, M. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 826-843
24. Trabuco, L. G.; Villa, E.; Schreiner, E.; Harrison, C. B.; Schulten, K. Methods 2009, 49, 174-180
25. Cheluvaraja, S.; Ortoleva, P. J. Chem. Phys. 2010, 132, 075102
26. Singharoy, A.; Cheluvaraja, S.; Ortoleva, P. J. J. Chem. Phys. 2011, 134, 044104
27. Singharoy, A.; Joshi, H.; Cheluvaraja, S.; Brown, D.; Ortoleva, P. J. Simulating Microbial Systems: Addressing Model uncertainty/incompleteness via Multiscaling and Entropy methods. In Microbial Systems Biology: Methods and Protocols; Navid, A., Ed.; Springer Science: New York, 2010; Vol. 881.
28. Jaqaman, K.; Ortoleva, P. J. J. Comput. Chem. 2002, 23, 484-491
29. Miao, Y.; Ortoleva, P. J. J. Comput. Chem. 2009, 30, 423-437
30. Pankavich, S.; Miao, Y.; Ortoleva, J.; Shreif, Z.; Ortoleva, P. J. J. Chem. Phys. 2008, 128, 234908-234920
31. Schmidt, E. Math. Ann. 1907, 63, 433-476
32. Singharoy, A.; Sereda, Y. V.; Ortoleva, P. J. J. Chem. Theory. Comput. 2012, DOI: http://dx.doi.org/10.1021/ct200574x
33. Miao, Y.; Ortoleva, P. J. Biopolymers 2010, 93, 61-73
34. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802
35. Shreif, Z.; Ortoleva, P. J. NSTI Nanotech. 2008, Nanotechnol. Conf. Trade Show, Tech. Proc. 2008, 3, 741-744
36. Shreif, Z.; Ortoleva, P. J. Comput. Math. Methods Med. 2009, 10, 49-70
37. Ortoleva, P. J.; Adhangale, P.; Cheluvaraja, S.; Fontus, M. W. A.; Shreif, Z. IEEE Eng. Med. Biol. 2009, 28, 70-79
38. Pankavich, S.; Shreif, Z.; Ortoleva, P. J. Phys. A 2008, 387, 4053-4069
39. Shreif, Z.; Ortoleva, P. J. Phys. A 2009, 388, 593-600
40. Ortoleva, P. J. J. Phys. Chem. B 2005, 109, 21258-21266
41. Miao, Y.; Ortoleva, P. J. J. Chem. Phys. 2006, 125, 44901-44908
42. Bose, S.; Ortoleva, P. J. J. Chem. Phys. 1979, 70, 3041-3056
43. Bose, S.; Ortoleva, P. J. Phys. Lett. A 1979, 69, 367-369
44. Bose, S.; Medina-Noyola, M.; Ortoleva, P. J. J. Chem. Phys. 1981, 75, 1762-1771
45. Shreif, Z.; Ortoleva, P. J. Stat. Phys. 2008, 130, 669-685
46. Pankavich, S.; Shreif, Z.; Miao, Y.; Ortoleva, P. J. J. Chem. Phys. 2009, 130, 194115-194124
47. Shreif, Z.; Pankavich, S.; Ortoleva, P. J. Phys. Rev. E 2009, 80, 031703
48. Pankavich, S.; Ortoleva, P. J. Math. Phys. 2010, 51, 063303-063316
49. Li, Z.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 6611-6615
50. Norris, G. E.; Anderson, B. F.; Baker, E. N. Acta Crystallogr., Sect. B 1991, 47, 998-1004
51. Gerstein, M.; Anderson, B. F.; Norris, G. E.; Baker, E. N.; Lesk, A. M.; Chothia, C. J. Mol. Biol. 1993, 234, 357-372
52. Miao, Y.; Johnson, J. E.; Ortoleva, P. J. J. Phys. Chem. B 2010, 114, 11181-11195