The color of rhodopsins at the ab initio multiconfigurational perturbation theory resolution

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 46, 2006, Pages 17154-17159

  Coto, Pedro B ^a   Strambi, Angela ^a   Ferré, Nicolas ^b   Olivucci, Massimo ^a,c  

^a UNIVERSITY OF SIENA   (Italy)

^b Institut de Chimie Biologique   (France)

^c BOWLING GREEN STATE UNIVERSITY   (United States)

Author keywords

Excited states; Quantum mechanics molecular mechanics

Indexed keywords

CARBOXYLIC ACID; RHODOPSIN;

AB INITIO CALCULATION; ABSORPTION; ARTICLE; CHROMATOPHORE; COLOR; ENERGY; MOLECULAR DYNAMICS; OPTICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN MODIFICATION; PROTEIN STRUCTURE; QUANTUM MECHANICS;

ANIMALS; CATTLE; COLOR; COMPUTATIONAL BIOLOGY; ELECTROSTATICS; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; RHODOPSIN;

BOS TAURUS;

EID: 33751249931     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0604048103     Document Type: Article

References (58)

1. Bolon DN, Mayo SL (2001) Proc Natl Acad Sci USA 98:14274-14279.
2. Dwyer MA, Looger LL, Hellinga HW (2004) Science 304:1967-1971.
3. Gherman BF, Goldberg SD, Cornish VW, Friesner RA (2004). J Am Chem Soc 126:7652-7664.
4. Roos BO (1987) in Advances in Chemical Physics: Ab Initio Methods in Quantum Chemistry, ed Lawley KP (Wiley, Chichester, UK), Vol 2, pp 399-445.
5. Andersson K, Malmqvist P-A, Roos BO, Sadlej AJ, Wolinski KJ (1990) Phys Chem 94:5483-5488.
6. Roos BO, Fülscher MP, Malmqvist P-A, Merchan M, Serrano- Andrés L (1995) in Quantum Mechanical Electronic Structure Calculations with Chemical Accuracy, ed Langhoff SR (Kluwer Academic, Dordrecht, The Netherlands), pp 357-438.
7. Garavelli M, Celani P, Bernardi F, Robb MA, Olivucci M (1997) J Am Chem Soc 119:11487-11494.
8. Gagliardi L, Roos BO (2005) Nature 433:848-851.
9. Ferré N, Olivucci M (2003) Theor Chem 632:71-82.
10. Warshel A (1976) Nature 260:679-683.
11. Warshel A, Chu ZT (2001) J Phys Chem B 105:9857-9871.
12. Gao J (1996) Acc Chem Res 29:298-305.
13. Andruniów T, Ferré N, Olivucci M (2004) Proc Natl Acad Sci USA 101:17908-17913.
14. Sinicropi A, Andruniów T, Ferré, N., Basosi R, Olivucci M (2005) J Am Chem Soc 127:11534-11535.
15. Honig B, Dinur U, Nakanishi K, Balogh-Nair V, Gavinowicz MA, Arnaboldi M, Motto MG (1979) J Am Chem Soc 101:7084-7086.
16. Hurley JB, Ebrey TG, Honig B, Ottolenghi M (1977) Nature 270:540-542.
17. Sakmar TP, Franke RR, Khorana HG (1989) Proc Natl Acad Sci USA 86:8309-8313.
18. Han W, Lin SW, Smith SO, Sakmar TP (1996) J Biol Chem 271:32330-32336.
19. Mathies RA, Lugtenburg J (2000) in Handbook of Biological Physics, ed Stavenga DG, de Grip WJ, Pugh EN (Elsevier, Amsterdam), Vol 3.
20. Blatz PE, Liebman P (1973) Exp Eye Res 17:573-580.
21. Kakitani H, Kakitani T, Rodman H, Honig B (1985) Photochem Photobiol 41:471-479.
22. Kropf A, Hubbard R (1958) Ann NY Acad Sci 74:266-280.
23. Neitz M, Neitz J, Jacobs GH (1991) Science 252:971-974.
24. Beppu Y, Kakitani T (1994) Photochem Photobiol 59:660-669.
25. Honig B, Greenberg AD, Dinur U, Ebrey TG (1976) Biochemistry 15:4593-4599.
26. Morton R (1955) Biochemistry 59:128-134.
27. Baasov T, Friedman N, Sheves M (1987) Biochemistry 26:3210-3217.
28. Kochendoerfer GG, Lin SW, Sakmar TP, Mathies RA (1999) Trends Biochem Sci 24:300-305.
29. Cembran A, Gonzáles-Luque R, Altoè, P, Merchán M, Bernardi F, Olivucci M, Garavelli M (2005) J Phys Chem A 109:6597-6605.
30. Mathies RA, Stryer L (1976) Proc Natl Acad sci USA 73:2169-2173.
31. Bonacic-Koutecky V, Köhler K, Michl J (1984) Chem Phys Lett 104:440-443.
32. Bonacic-Koutecky V, Schöffel KJ, Michl J (1987) Theor Chim Acta 72:459-474.
33. Birge RR, Murray LP, Pierce BM, Akita H, Balogh-Nair V, Findsen LA, Nakanishi K (1985) Proc Natl Acad Sci USA 82:4117-4121.
34. Arnaboldi M, Motto MG, Tsujimoto K, Balogh-Nair V, Nakanishi K (1979) J Am Chem Soc 101:7082-7084.
35. Warshel A (1979) J Phys Chem 83:1640-1652.
36. Padrón-García JA, Crespo-Otero R, Hernández- Rodríguez EW, Garriga P, Montera LA, Garcia-Pineiro JC (2004) Proteins 57:392-399.
37. Jacobs GH, Deegan JF, Jr, Tan Y, Li W-H (2002) Vision Res 42:11-18.
38. Jacobs GH, Deegan II, J. F (2003) Vision Res 43:227-236.
39. Wanko M, Hoffmann M, Strodel P, Koslowski A, Thiel W, Neese F, Frauenheim T, Elstner M (2005) J Phys Chem B 109:3606-3615.
40. Warshel A, Chu ZT, Hwang J-K (1991) Chem Phys 158:303-314.
41. Houjou H, Inoue Y, Sakurai M (2001) J Phys Chem B 105:867-879.
42. Matsuura A, Sato H, Houjou H, Saito S, Hayashi T, Sakurai M (2006) J Comp Chem 27:1623-1630.
43. Vreven T, Morokuma K (2003) Theor Chem Acc 109:125-132.
44. Rajamani R, Gao J (2002) J Comp Chem 23:96-105.
45. Yamada A, Kakitani T, Yamamoto S, Yamato T (2002) Chem Phys Lett 366:670-675.
46. Hayashi S, Ohmine I (2000) J Phys Chem B 104:10678-10691.
47. Hayashi S, Tajkhorshid E, Pebay-Peyroula E, Royant A, Landau EM, Navarro J, Schulten K (2001) J Phys Chem B 105:10124-10131.
48. Hayashi S, Tajkhorshid E, Schulten K (2002) Biophys J 83:1281-1297.
49. Fujimoto K, Jun-ya H, Hayashi S, Shigeki K, Nakatsuji H (2005) Chem Phis Lett 414:239-242.
50. Hoffmann M, Wanko M, Strodel P, König PH, Frauenheim T, Schulten K, Thiel W, Tajkhorshid E, Elstner M (2006) J Am Chem Soc 128:10808-10818.
51. Teller DC, Okada T, Behnke CA, Palczewski K, Stenkamp RE (2001) Biochemistry 40:7761-7772.
52. Singh UC, Kollman PA (1986) J Comp Chem 7:718-730.
53. Ren L, Martin CH, Wise KJ, Gillespie NB, Luecke H, Lanyi J, Spudich JL, Birge RR (2001) Biochemistry 40:13906-13914.
54. Fahmy K, Jager F, Beck M, Zvyaga TA, Sakmar TP, Siebert F (1993) Proc Nat Acad Sci USA 90:10206-10210.
55. Okada T, Sughihara M, Bondar A-N, Elstner M, Entel P, Buss V (2004) J Mol Biol 342:571-583.
56. Furutani Y, Shichida Y, Kandori H (2003) Biochemistry 42:9619-9625.
57. Andersson K, Blomberg MRA, Fülscher MP, Karlstöm G, Lundh R, Malmqvist P-A, Neogrády P, Olsen J, Roos BO, Sadlej AJ, et al. (2002) MOLCAS 6.1 (University of Lund, Lund, Sweden).
58. Verdegem PJE, Bovee-Geurts PHM, De-Grip WJ, Lugtenburg J, De-Groot HJM (1999) Biochemistry 38:11316-11324.