Semiempirical configuration interaction calculations in biochemical environments: Parametrization and application to γd-crystallin, an eye-lense protein

Biophysical Chemistry

Volumn 153, Issue 2-3, 2011, Pages 173-178

  Kruse, Sandra ^a   Krapf, Sebastian ^a   Lampe, Benjamin ^a   Koslowski, Thorsten ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

Charge transfer; Configuration interaction; Eye lense protein; Optical absorption; Semiempirical model; Simulation; Theory

Indexed keywords

DELTA CRYSTALLIN; GAMMA CRYSTALLIN;

ARTICLE; ATOM; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; ELECTRONICS; MATHEMATICAL ANALYSIS; OPTICS; PARAMETRIZATION; PRIORITY JOURNAL;

CRYSTALLINS; GAMMA-CRYSTALLINS; HUMANS; MODELS, MOLECULAR; MOLECULAR CONFORMATION;

EID: 78651066769     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2010.11.005     Document Type: Article

References (68)

1. G.R. Fleming, and R. van Grondelle Phys. Today 47 1994 48
2. T. Ritz, A. Damjanovic, and K. Schulten Chemphyschem 3 2002 243
3. R.E. Blankenship Molecular Mechanisms of Photosynthesis 2002 Blackwell Oxford
4. S. Weber BBA Bioenerg. 1707 2005 1
5. R.R. Birge Annu. Rev. Phys. Chem. 41 1990 683
6. W.D. Hoff, K.-H. Jung, and J.L. Spudich Annu. Rev. Biophys. Biomol. Struct. 26 1997 223
7. T. Biskup, E. Schleicher, A. Okafuji, G. Link, K. Hitomi, E.D. Getzoff, and S. Weber Angew. Chem. Int. Ed. 48 2009 404
8. Schulten K. Festkörperprobleme 22 Treusch J. 1982 Vieweg Braunschweig 61
9. T. Ritz, S. Adem, and K. Schulten Biophys. J. 78 2000 707
10. T. Ritz, P. Thalau, J.B. Phillips, R. Wiltschko, and W. Wiltschko Nature 429 2004 177
11. S. Günes, H. Neugebauer, and N.S. Sariciftci Chem. Rev. 107 2007 1324
12. M.P. Fülscher, L. Serrano-Andres, and B.O. Roos J. Am. Chem. Soc. 119 1997 6168
13. C. Hättig J. Grotendorst, S. Blügel, D. Marx, Computational Nanoscience: Do It Yourself! John von Neumann institute Jülich NIC Series 31 2006 245
14. A. Dreuw, and M. Head-Gordon Chem. Rev. 105 2005 4009
15. J. Neugebauer J. Phys. Chem. B 112 2008 2207
16. D. Möbius Adv. Mater. 7 1995 437
17. T. Kobayashi J-aggregates 1996 World Scientific Singapore
18. O. Mülken, L. Mühlbacher, T. Schmid, and A. Blumen Phys. Rev. E 81 2010 41114
19. P. Nalbach, and M. Thorwart J. Chem. Phys. 132 2010 194111
20. K.K. Sharma, and P. Santhoshkumar BBA 1790 2009 1095
21. L. Takemoto, and C.M. Sorensen Exp. Eye Res. 87 2008 496
22. H. Bloemendal, W. de Jong, R. Jaenicke, N.H. Lubsen, C. Slingsby, and A. Tardieu Progr. Biophys. Mol. Biol. 86 2004 407
23. H. Bloemendal CRC Crit. Rev. Biochem. 12 1982 1
24. A. Laganowsky, and D. Eisenberg Protein Sci. 19 2010 1978
25. A. Laganowsky, J.L. Benesch, M. Landau, L. Ding, M.R. Sawaya, D. Cascio, Q. Huang, C.V. Robinson, J. Horwitz, and D. Eisenberg Protein Sci. 19 2010 1031
26. C. Bagneris, O.A. Bateman, C.E. Naylor, N. Cronin, W.C. Boelens, N.H. Keep, and C. Slingsby J. Mol. Biol. 392 2009 1242
27. V. Nalini, B. Bax, H.P. Driessen, D.S. Moss, P.F. Lindley, and C. Slingsby J. Mol. Biol. 236 1994 1250
28. S. Najmudin, V. Nalini, H.P. Driessen, C. Slingsby, T.L. Blundell, D.S. Moss, and P.F. Lindley Acta Crystallogr. D 49 1993 223
29. L.M. Sampaleanu, F. Vallee, C. Slingsby, and P.L. Howell Biochemistry 40 2001 2732
30. O.A. Bateman, A.G. Purkiss, R. van Montfort, C. Slingsby, C. Graham, and G. Wistow Biochemistry 42 2003 4349
31. J. Wang, X. Zuo, P. Yu, I.J. Byeon, J. Jung, X. Wang, M. Dyba, S. Seifert, C.D. Schweiters, J. Qin, A.M. Gronenborn, and Y.X. Wang J. Am. Chem. Soc. 131 2009 10507
32. J. Wang, P. Cieplak, and P.A. Kollman J. Comp. Chem. 21 2000 1049
33. P. Ren, and J.W. Ponder J. Phys. Chem. B 107 2003 5933
34. A. Huizinga, A.C.C. Bot, F.F.M. de Mul, G.F.J.M. Gijs, and J. Greve Exp. Eye Res. 48 1989 487 and references therein
35. V. Hornak, R. Abel, R. Okur, B. Strockbine, A. Roitberg, and C. Simmerling Proteins: Struct. Funct. Bioinf. 65 2006 712
36. R. Pariser, and R.G. Parr J. Chem. Phys. 21 1953 466
37. R. Pariser, and R.G. Parr J. Chem. Phys. 21 1953 767
38. J.A. Pople Proc. Phys. Soc. A 68 1955 81
39. A. Warshel, and M. Karplus J. Am. Chem. Soc. 94 1972 5612
40. J. Lobaugh, and P.J. Rossky J. Phys. Chem. A 103 1999 9432
41. J. Lobaugh, and P.J. Rossky J. Phys. Chem. A 104 2000 899
42. A. Takahashi, and S. Mukamel J. Chem. Phys. 100 1994 2366
43. P. Tavan, and K. Schulten Phys. Rev. B 36 1987 4337
44. K. Nishimoto, and N. Mataga Z. Phys. Chem. 12 1957 335
45. J.C. Slater, and G.F. Koster Phys. Rev. 94 1954 1498
46. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein J. Chem. Phys. 79 1983 926
47. J. Ladik, and K. Appel Theor. Chim. Acta 4 1966 132
48. T. Cramer, S. Krapf, and T. Koslowski J. Phys. Chem. B 108 2004 11812
49. T. Cramer, T. Steinbrecher, A. Labahn, and T. Koslowski PCCP 7 2005 4039
50. B.O. Roos, K. Andersson, and M.P. Fülscher Chem. Phys. Lett. 192 1992 5
51. J. Lorentzon, P.-Å. Malmqvist, M. Fülscher, and B.O. Roos Theor. Chem. Acc. 91 1995 91
52. L. Serrano-Andrés, and B.O. Roos J. Am. Chem. Soc. 118 1996 185
53. J.P. Hare, H.W. Kroto, and R. Taylor Chem. Phys. Lett. 177 1991 394
54. 1 = 0.45 eV (next-nearest neighbours, no electron-phonon coupling)
55. This corresponds to the smallest value for which the SCF procedure converged.
56. P. Dean, and R.J. Bell Discuss. Faraday Soc. 50 1970 55
57. T. Koslowski, and W. von Niessen Phys. Rev. B 42 1990 10342
58. T. Koslowski, and W. von Niessen J. Phys. Condens. Matter 4 1992 6109
59. B.T. Smith, J.M. Boyle, J.J. Dongerra, B.S. Garbow, Y. Ikebe, V.C. Uleba, and C.B. Moler Matrix Eigensystem Routines - EISPACK Guide 1976 Springer Berlin-Heidelberg-New York
60. B.S. Garbow, J.M. Boyle, J.J. Dongerra, and C.B. Moler Matrix Eigensystem Routines - EISPACK Guide Extension 1977 Springer Berlin-Heidelberg-New York
61. C. Lanczos J. Res. NBS B 45 1950 225
62. J.K. Cullum, and R. Willoughby Lanczos Algorithms For Large Symmetric Eigenvalue Problems I + II 1985 Birkhäuser Boston-Basel-Stuttgart
63. T. Koslowski, and W. von Niessen J. Comp. Chem. 14 1993 769
64. I. Ohmine, M. Karplus, and K. Schulten J. Chem. Phys. 68 1978 2298
65. J. Florian, and A. Warshel J. Phys. Chem. B 101 1997 5583
66. M.A. Thompson, and M.C. Zerner J. Am. Chem. Soc. 113 1991 8210
67. K. Wang, C. Cheng, L. Li, H. Liu, Q. Huang, C. Xia, K. Yao, P. Sun, J. Horwitz, and X. Gong Investig. Ophthalmol. Vis. Sci. 48 2007 3719
68. H.R. Taylor, S.K. West, F.S. Rosenthal, B. Muñoz, H.S. Newland, H. Abbey, and E.A. Emmett N. Engl. J. Med. 319 1988 1429