Modeling reaction routes from rhodopshin to bathorhodopsin

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 3, 2010, Pages 614-622

  Khrenova, M G ^a   Bochenkova, A V ^a   Nemukhin, A V ^a,b  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b EMANUEL INSTITUTE OF BIOCHEMICAL PHYSICS   (Russian Federation)

Author keywords

Bathorhodopsin; Molecular modeling; Photoactivation; QM MM; Rhodopsin; Thermal activation

Indexed keywords

BATHORHODOPSIN; ETHYLENE; RHODOPSIN;

ACCURACY; ARTICLE; CRYSTAL STRUCTURE; DENSITY FUNCTIONAL THEORY; ENERGY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUANTUM CHEMISTRY; QUANTUM MECHANICS; THEORETICAL MODEL; VIBRATION; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; HYDROGEN BOND; PROTEIN CONFORMATION; QUANTUM THEORY; RAMAN SPECTROMETRY;

HYDROGEN BONDING; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; QUANTUM THEORY; RHODOPSIN; SPECTRUM ANALYSIS, RAMAN;

EID: 77949894983     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.l002/prot.22590     Document Type: Article

References (51)

1. Kandori H, Shichida Y, Yoshizawa T. Photoisomerization in rhodopsin. Biochemistry (Moscow) 2001;66:1197-1209.
2. Kandori H, Shichida Y, Yoshizawa T. Absolute absorption spectra of batho- and photorhodopsins at room temperature picosecond laser photolysis of rhodopsin in Polyacrylamide. Biophys J 1989;6:453-457.
3. Shichida Y, Matuoka S, Yoshizawa T. Formation of photorhodopsin, a precursor of bathorhodopsin, detected by a picosecond laser photolysis at room temperature. Photobiochem Photobiophys 1984;7: 221-228.
4. Kukura P, McCamant DW, Yoon S, Wandschneider DB, Mathies RA. Structural observation of the primary isomerization in vision with femtosecond-stimulated Raman. Science 2005;310:1006-1009.
5. Loppnow GR, Mathies RA. Excited-state structure and isomerization dynamics of the retinal chromophore in rhodopsin from resonance Raman intensities. Biophys J 1988;54:35-43.
6. Pan D, Ganim. Z, Kim JE, Verhoeven MA, Lugtenburg J, Mathies RA. Time-resolved resonance Raman analysis of chromophore structural changes in the formation and decay of rhodopsin's BSI Intermediate. J Am Chem. Soc 2002;124:4857-4864.
7. 12 torsion coordinate. J Phys Chem B 1998;102:787-1280
8. Jäger F, Ujj L, Atkinson GH. Vibrational spectrum of bathorhodopsin in the room-temperature rhodopsin photoreaction. J Am Chem Soc .1997;119:12610-12618.
9. Nakamichi H, Okada T. Crystallographic analysis of primary visual photochemistry. Angew Chem Int Ed Engl 2006;45:4270-4273.
10. Nakamichi H, Okada T. Local peptide movement in the photoreaction intermediate of rhodopsin. Proc Natl Acad Sci USA 2006;103; 12729-12734.
11. Warshel A. Bicycle-pedal model for 1st step in vision process. Nature 1976;260:679-683.
12. Warshel A, Barboy N. Energy-storage and reaction pathways in the first step of the vision process. J Am Chem Soc 1982;104:1469-1476.
13. Warshel A, Chu ZT, Hwang JK. The dynamics of the primary event in rhodopsins revisited. Chem Phys 1991;158:303-314.
14. Warshel A. Molecular Dynamics Simulations of Biological Reactions. Acc Chem Res 2002;35:385-395.
15. Liu RHS, Asato AE. The primary process of vision and the structure of bathorhodopsin: a mechanism for photoisomerization of polyenes Proc Natl Acad Sci USA 1985;82:259-263.
16. Liu RHS. Photoisomerization by Hula-Twist: A Fundamental Supramolecular Photochemical Reaction. Acc Chem Res 2001;34:555-562.
17. Andruniow T, Ferre N, Olivucci M, Structure, initial, excited-state relaxation, and energy storage of rhodopsin resolved at the multiconfigurational perturbation theory level. Proc Natl Acad. Sci USA. 2004;101:17908-17913.
18. Frutos LM, Andruniow T, Santoto F, Ferre N, Olivucci M. Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum, chemistry. Proc Natl Acad Sci USA 2007;104:7764-7769.
19. Strambi A, Coto PB, Frutos LM, Ferré N, Olivucci M. Relationship between the excited state relaxation paths of rhodopsin and isorhodopsin. J Am Chem Soc 2008;130:3382-3388.
20. Schapiro I, Weingart O, Buss V. Bicycle-pedal isomerization in a rhodopsin chromophore model. J Am Chem Soc 2009;131:16-17.
21. Weingart O. The twisted C11C12 bond of the rhodopsin chromophore a photochemical hot spot. J Am Chem Soc 2007;129:10618-10619.
22. Altun A, Yokoyama S, Morokuma K. Mechanism of spectral tuning going from retinal in vacuo to bovine rhodopsin and its mutants: multireference ab initio quantum mechanics/molecular mechanics studies. J Phys Chem B 2008;12:16883-16890.
23. Blomgren F, Larson S. Primary photoprocess in vision: minimal motion to reach the photo- and bathorhodopsin Intermediates. J Phys Chem B 2005;109:9104-9110. (Pubitemid 40750947)
24. Nakatsuji H, Hasegawa J, Hayashi S, Fujimoto K. Theoretical studies on the color-tuning mechanism in retinal proteins. J Chem. Theory Comput 2007;3:605-618.
25. Muñoz-Losa A, Galván IF, Aguilar MA, Martin ME. Retinal models: comparison of electronic absorption spectra in the gas phase and on methanol solution. J Phys Chem B 2008;112:8815-8823.
26. Tomasello G, Olaso-González G, Altoè P, Stenta M, Serrano-Andrés L, Merchán M, Oriandi G, Bottoni An, Garavelli M. Electrostatic control of the photoisomerization efficiency and optical properties in visual pigments: on the role of counterion quenching. J Am Chem Soc 2009;131:5172-5186.
27. Ala-Laurila P, Donner K, Koskeiainen A. Thermal Activation and Photoactivation of Visual Pigment. Biophys J 2004;86:3653-3662.
28. Baylor DA, Nunn BJ, Schnapf JL. The photoeurrent, noise and spectral sensitivity of rods of the monkey Macaca Fasciculars J Phisiol 1984;357:575-607.
29. Cooper Al. Energy uptake in the first step of visual excitation. Nature 1979;282:531-533.
30. Schick GAl, Cooper TM, Hoiloway RA, Murray LP, Birge RR. Energy storage in the primary photochemical events of rhodopsin. and isorhodopsin. Biochemistry 1987;26:2556-2562.
31. Boucher F, Leblanc RM. Energy storage in the primary photoreaction of the bovine rhodopsin. A photoacoustic study. Photochem Photobiol 1985;41:459-1165
32. Warshel A, Levitt M. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 1976;103:227-249.
33. 1 excitation in protein, in solution, and in the gas phase. J Am Chem Soc 2007;129:13035-13042.
34. Gascon JA, Batista VS. QM/MM study of energy storage and molecular rearrangements due to the primary event in vision. Biophys J 2004;87:2931-2941.
35. Gascón. JA, Sproviero EM, Batista VS. Computational studies of the primary phototransduction event in visual, rhodopsin. Acc Chem Res 2006;39:184-193
36. 1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method. Theor Chem Acc 2003;109:125-132.
37. Schreiber IM, Sugihara M, Okada T, Buss V. Quantum mechanical studies on the crystallographic model, of bathorhodopsin. Angew Chem Int Ed 2006;45:4274-4277.
38. Teller DC, Okada T, Behnke CA, Palczewski K, Stenkamp RE. Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs). Biochemistry 2001;40:7761-7777.
39. Okada T, Suguihara M, Bondar A-N, Elstner M, Entel P, Buss V. The retinal conformation and its environment in rhodopsin in light of a new 2.2 Å crystal structure. J Mol Biol 2004;342:571-583.
40. Bakowies D, Thiel W. Hybrid models for combined quantum, mechanical and molecular mechanical approaches. J Phys Chem 1996; 100; .10580-10594.
41. Adamo C, Barone V. Toward reliable density functional methods without adjustable parameters: The PBEO model. J Chem Phys 1999;110:6158-6170,
42. Grafenstein J, Kraka El, Filatov M, Cremer D. Can unrestricted density functional theory describe open shell singlet biradicals? Int J Mol Sci 2002;3:360-394.
43. Röhrig UF, Daniel Sebastiani D. NMR Chemical Shifts of the Rhodopsin Chromophore in the Dark State and in Bathorhodopsin: A. Hybrid QM/MM Molecular Dynamics Study. J Phys Chem B 2008;112:1267-1274.
44. Wang J, Cieplak P, Kollman PA. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 2000;21:1049-1074.
45. Li H, Jensen JH. Partial Hessian vibrational analysis. Theor Chem Acc 2002;107:211-219.
46. 1 photo-absorption in biological, chromophores. Proc SPIE 2007;6449:64490N.
47. Bravaya KB, Bochenkova. AV, Granovsky AA, Savitsky AP, Nemukhin AV. Modeling photoabsorption, of the asFP595 chromophore. J Phys Chem A 2008;112;8804-8810.
48. Witek HA, Choe YK, Finley JP, Hirao K. Intruder state avoidance multireference Mflller-Plesset perturbation theory. J Comp Chem 2002;23:957-965.
49. Gordon MS, Freitag MA, Bandyopadhyay P, Jensen JH, Kairys V, Stevens W. The effective fragment potential method: a QM-based MM approach to modeling environmental effects in chemistry. J Phys Chem A 2001;105:293-307. (Pubitemid 32159158)
50. Epifanovsky E, Polyakov I, Grigorenko B, Nemukhin A, Kryiov A. Quantum, chemical benchmark studies of the electronic properties of the green fluorescent protein chromophore: Part I. Electronically excited and ionized states of the anionic chromophore in the gas phase. J Chem Theor Comp 2009;5:1895-1906.
51. Birge RR, Cooper TM. Energy storage in the primary step of the photocycle of bacteriorhodopsin. Biophys J .1983;42:61-69.