Interpolation schemes for peptide rearrangements

Journal of Chemical Physics

Volumn 132, Issue 5, 2010, Pages

  Bauer, Marianne S ^a   Strodel, Birgit ^b   Fejer, Szilard N ^a   Koslover, Elena F ^c   Wales, David J ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b FORSCHUNGSZENTRUM JÜLICH   (Germany)

^c STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARTESIAN COORDINATE; CO-ORDINATE SYSTEM; DIHEDRAL ANGLES; DISTANCE METRICS; INTERNAL COORDINATES; INTERPOLATION SCHEMES; NATURAL COORDINATES; UNITED ATOM FORCE FIELD;

ALIGNMENT;

INTERPOLATION;

PEPTIDE;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; CHEMISTRY; COMPUTER ASSISTED DIAGNOSIS; COMPUTER SIMULATION; IMAGE ENHANCEMENT; MATHEMATICS; METHODOLOGY; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN FOLDING; THERMODYNAMICS;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTER SIMULATION; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; MATHEMATICS; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; PEPTIDES; PROTEIN CONFORMATION; PROTEIN FOLDING; THERMODYNAMICS;

EID: 76349114307     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3273617     Document Type: Article

References (63)

1. F. Nó and S. Fischer, Curr. Opin. Struct. Biol. 0959-440X 18, 154 (2008). 10.1016/j.sbi.2008.01.008
2. D. Prada-Gracia, J. Gómez-Gardenes, P. Echenique, and F. Fernando, PLOS Comput. Biol. 1553-734X 5, e1000415 (2009). 10.1371/journal.pcbi.1000415
3. R. E. Kunz and R. S. Berry, J. Chem. Phys. 0021-9606 103, 1904 (1995). 10.1063/1.469714
4. D. J. Wales, Mol. Phys. 0026-8976 100, 3285 (2002). 10.1080/ 00268970210162691 (Pubitemid 35446132)
5. D. J. Wales, Mol. Phys. 0026-8976 102, 891 (2004). 10.1080/ 00268970410001703363
6. D. J. Wales and J. P. K. Doye, J. Chem. Phys. 0021-9606 119, 12409 (2003). 10.1063/1.1625644
7. D. Wales, Int. Rev. Phys. Chem. 0144-235X 25, 237 (2006). 10.1080/01442350600676921
8. D. J. Wales, Energy Landscapes (Cambridge University Press, Cambridge, 2003).
9. V. S. Pande and D. S. Rokhsar, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 96, 1273 (1999). 10.1073/pnas.96.4.1273 (Pubitemid 29098441)
10. W. Swope, J. Pitera, F. Suits, M. Pitman, M. Eleftheriou, B. Fitch, R. Germain, A. Rayshubski, T. Ward, Y. Zhestkov, and R. Zhou, J. Phys. Chem. B 1089-5647 108, 6582 (2004). 10.1021/jp037422q
11. S. V. Krivov and M. Karplus, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 101, 14766 (2004). 10.1073/pnas.0406234101 (Pubitemid 39410749)
12. J. N. Murrell and K. J. Laidler, Trans. Faraday Soc. 0014-7672 64, 371 (1968). 10.1039/tf9686400371
13. D. J. Wales, OPTIM, a program for optimizing geometries and calculating pathways, http://www-wales.ch.cam.ac.uk/software.html, 2009.
14. W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 0163-1829 66, 052301 (2002). 10.1103/PhysRevB.66.052301
15. B. Peters, A. T. Bell, and A. Chakraborty, J. Chem. Phys. 0021-9606 121, 4453 (2004). 10.1063/1.1778161
16. E. F. Koslover and D. J. Wales, J. Chem. Phys. 0021-9606 127, 134102 (2007). 10.1063/1.2767621 (Pubitemid 47534190)
17. S. A. Trygubenko and D. J. Wales, J. Chem. Phys. 0021-9606 120, 2082 (2004). 10.1063/1.1636455
18. R. Elber and M. Karplus, Chem. Phys. Lett. 0009-2614 139, 375 (1987). 10.1016/0009-2614(87)80576-6
19. R. Czerminski and R. Elber, J. Chem. Phys. 0021-9606 92, 5580 (1990). 10.1063/1.458491
20. G. Henkelman and H. Jónsson, J. Chem. Phys. 0021-9606 111, 7010 (1999). 10.1063/1.480097
21. G. Henkelman, B. P. Uberuaga, and H. Jónsson, J. Chem. Phys. 0021-9606 113, 9901 (2000). 10.1063/1.1329672 (Pubitemid 32076883)
22. G. Henkelman and H. Jónsson, J. Chem. Phys. 0021-9606 113, 9978 (2000). 10.1063/1.1323224 (Pubitemid 32076892)
23. G. Henkelman and H. Jónsson, J. Chem. Phys. 0021-9606 115, 9657 (2001). 10.1063/1.1415500 (Pubitemid 33147327)
24. J. Baker and F. Chan, J. Comput. Chem. 0192-8651 17, 888 (1996). 10.1002/(SICI)1096-987X(199605)17:7<888::AID-JCC12>3.0.CO;2-7
25. P. Pulay, G. Foragasi, F. Pang, and J. E. Boggs, J. Am. Chem. Soc. 0002-7863 101, 2550 (1979). 10.1021/ja00504a009
26. P. Pulay and G. Fogarasi, J. Chem. Phys. 0021-9606 96, 2856 (1992). 10.1063/1.462844
27. G. Fogarasi, X. Zhou, P. W. Taylor, and P. Pulay, J. Am. Chem. Soc. 0002-7863 114, 8191 (1992). 10.1021/ja00047a032
28. E. F. Koslover and D. J. Wales, J. Chem. Phys. 0021-9606 127, 234105 (2007). 10.1063/1.2807227
29. Y. Duan, C. Wu, S. Chowdhury, M. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, and T. Lee, J. Comput. Chem. 0192-8651 24, 1999 (2003). 10.1002/jcc.10349
30. E. Neria, S. Fischer, and M. Karplus, J. Chem. Phys. 0021-9606 105, 1902 (1996). 10.1063/1.472061
31. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. S. Swaminathan, and M. Karplus, J. Comput. Chem. 0192-8651 4, 187 (1983). 10.1002/jcc.540040211
32. Intcor.doc, http://www.lobos.nih.gov/charmm, 2002.
33. M. Balbirnie, R. Grothe, and D. S. Eisenberg, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 98, 2375 (2001). 10.1073/pnas.041617698 (Pubitemid 32209490)
34. R. Nelson, M. R. Sawaya, M. Balbirnie, A. O. Madsen, C. Riekel, R. Grothe, and D. Eisenberg, Nature (London) 0028-0836 435, 773 (2005). 10.1038/nature03680 (Pubitemid 40839722)
35. A. G. Cochran, N. J. Skelton, and M. A. Starovasnik, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 98, 5578 (2001). 10.1073/pnas.091100898 (Pubitemid 32435684)
36. C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 101, 4077 (2004). 10.1073/pnas.0305260101 (Pubitemid 38405886)
37. P. Valtazanos and K. Ruedenburg, Theor. Chim. Acta 0040-5744 69, 281 (1986). 10.1007/BF00527705
38. J. Nocedal, Math. Comput. 0025-5718 35, 773 (1980). 10.2307/2006193
39. D. Liu and J. Nocedal, Math. Program. 0025-5610 45, 503 (1989). 10.1007/BF01589116
40. D. Sheppard, R. Terrell, and G. Henkelman, J. Chem. Phys. 0021-9606 128, 134106 (2008). 10.1063/1.2841941
41. L. J. Munro and D. J. Wales, Phys. Rev. B 0163-1829 59, 3969 (1999). 10.1103/PhysRevB.59.3969
42. Y. Kumeda, L. J. Munro, and D. J. Wales, Chem. Phys. Lett. 0009-2614 341, 185 (2001). 10.1016/S0009-2614(01)00334-7 (Pubitemid 33630794)
43. Y. Kumeda and D. J. Wales, Chem. Phys. Lett. 0009-2614 374, 125 (2003). 10.1016/S0009-2614(03)00668-7 (Pubitemid 36613943)
44. E. Dijkstra, Numer. Math. 0029-599X 1, 269 (1959). 10.1007/BF01386390
45. J. M. Carr, S. A. Trygubenko, and D. J. Wales, J. Chem. Phys. 0021-9606 122, 234903 (2005). 10.1063/1.1931587 (Pubitemid 40925786)
46. K. Ńmeth, O. Coulaud, G. Monard, and J. G. ngyán, J. Chem. Phys. 0021-9606 113, 5598 (2000). 10.1063/1.1290611 (Pubitemid 30958941)
47. E. F. Koslover, M.Phil. thesis, University of Cambridge, Cambridge, 2007.
48. E. B. Wilson, J. C. Decius, and P. C. Cross, Molecular Vibrations (Dover, New York, 1980).
49. I. N. Shindyalov and P. E. Bourne, Protein Eng. 0269-2139 11, 739 (1998). 10.1093/protein/11.9.739
50. F. Teichert, U. Bastello, and M. Porto, BMC Bioinf. 1471-2105 8, 425 (2007). 10.1186/1471-2105-8-425 (Pubitemid 351315022)
51. W. R. Taylor and C. A. Orengo, J. Mol. Biol. 0022-2836 208, 1 (1989). 10.1016/0022-2836(89)90084-3 (Pubitemid 19191513)
52. P. R. Bunker and P. Jensen, Molecular Symmetry and Spectroscopy, 2nd ed. (NRC Research, Ottawa, 1998).
53. E. Maolepsza, B. Strodel, M. Khalili, S. Trygubenko, S. Fejer, and D. J. Wales, " Symmetrisation of the AMBER and CHARMM force fields.," J. Comput. Chem. 0192-8651 (in press).
54. See supplementary material at http://dx.doi.org/10.1063/1.3273617 E-JCPSA6-132-059948 for details of the DNEB parameters and the tests used to compare alignment according to distance metrics and the fixed hydrogen labels.
55. R. E. Leone and P. v. R. Schleyer, Angew. Chem., Int. Ed. Engl. 0570-0833 9, 860 (1970). 10.1002/anie.197008601
56. F. Nó, F. Ille, J. C. Smith, and S. Fischer, Proteins: Struct., Funct., Bioinf. 1097-0134 59, 534 (2005). 10.1002/prot.20422 (Pubitemid 40594297)
57. B. Strodel, C. S. Whittleston, and D. J. Wales, J. Am. Chem. Soc. 0002-7863 129, 16005 (2007). 10.1021/ja075346p
58. T. Lazaridis and M. Karplus, Proteins: Struct., Funct., Genet. 0087-3585 35, 133 (1999). 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0. CO;2-N
59. A. Onufriev, D. Bashford, and D. A. Case, Proteins 0887-3585 55, 383 (2004). 10.1002/prot.20033 (Pubitemid 38437495)
60. D. Case, T. Darden, T. C. Cheatham III, C. Simmerling, J. Wang, R. Duke, R. Luo, K. Merz, D. Pearlman, M. Crowley, R. Walker, W. Zhang, B. Wang, S. Hayik, A. Roitberg, G. Seabra, K. Wong, F. Paesani, X. Wu, S. Brozell, V. Tsui, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, P. Beroza, D. Mathews, C. Schafmeister, W. Ross and P. Kollman, AMBER9, University of California, 2006.
61. D. Pearlman, D. Case, J. Caldwell, W. Ross, T. C. Cheatham III, S. DeBolt, D. Ferguson, G. Seibel, and P. Kollman, Comput. Phys. Commun. 0010-4655 91, 1 (1995). 10.1016/0010-4655(95)00041-D
62. D. Case, T. C. Cheatham III, T. Darden, H. Gohlke, R. Luo, K. M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang, and R. Woods, J. Comput. Chem. 0192-8651 26, 1668 (2005). 10.1002/jcc.20290 (Pubitemid 43076180)
63. J. M. Carr and D. J. Wales, J. Phys. Chem. B 1089-5647 112, 8760 (2008). 10.1021/jp801777p