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Том 17   Выпуск 2   Год 2022
Список литературы

  1. Spudich J.L., Yang C.S., Jung K.H., Spudich E.N. Retinylidene Proteins: Structures and Functions from Archaea to Humans. Annu. Rev. Cell Dev. Biol. 2000;16:365–392. doi: 10.1146/annurev.cellbio.16.1.365
  2. Helmreich E.J.M., Hofmann K.-P. Structure and function of proteins in G-protein-coupled signal transfer. BBA. 1996;1286(3):285–322. doi: 10.1016/S0304-4157(96)00013-5
  3. Shichida Y., Matsuyama T. Evolution of opsins and phototransduction. Phil. Trans. R. Soc. B. 2009;364(1531):2881–2895. doi: 10.1098/rstb.2009.0051
  4. Shichida Y., Imai H. Visual pigment: G-protein-coupled receptor for light signals. Cell. Mol. Life Sci. 1998;54:1299–1315. doi: 10.1007/s000180050256
  5. Palczewski K. G Protein–Coupled Receptor Rhodopsin. Annual Review of Biochemistry. 2006;75:743–767. doi: 10.1146/annurev.biochem.75.103004.142743
  6. Menon S.T., Han M., Sakmar T.P. Rhodopsin: Structural Basis of Molecular Physiology. Physiol. Rev. 2001;81:1659–1688. doi: 10.1152/physrev.2001.81.4.1659
  7. Lamb T., Collin S., Pugh E.N.Jr. Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nat. Rev. Neurosci. 2007;8:960–976. doi: 10.1038/nrn2283
  8. Rieke F., Baylor D.A. Origin of Reproducibility in the Responses of Retinal Rods to Single Photons. Biophysical Journal. 1998;75(4):1836–1857. doi: 10.1016/S0006-3495(98)77625-8
  9. Sakmar T.P., Menon S.T., Marin E.P., Awad E.S. Rhodopsin: Insights from Recent Structural Studies. Annual Reviews. 2002;31(1):443-484. doi: 10.1146/annurev.biophys.31.082901.134348
  10. Yan B., Spudich J.L., Mazur P., Vunnam S., Derguini F., Nakanishi K.J. Spectral Tuning in Bacteriorhodopsin in the Absence of Counterion and Coplanarization Effects. Biol. Chem. 1995;270(50):29668–29670. doi: 10.1074/jbc.270.50.29668
  11. Liu R.S.H., Krogh E., Li X.-Y., Mead D., Colmenares L.U., Thiel J.R., Ellis J., Wong D., Asato A.E. Analyzing the red-shift characteristics of azulenic, naphthyl, other ring-closed and retinyl pigment analogs of bacteriorhodopsin. Photochem. Photobiol. 1993;58(5):701–705. doi: 10.1111/j.1751-1097.1993.tb04955.x
  12. Tomasello G.T., Olaso-González G., Altoè P., Stenta M., Serrano-Andrés L., Merchán M., Orlandi G., Bottoni A., 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(14):5172–5186. doi: 10.1021/ja808424b
  13. Wanko M., Hoffmann M., Frahmcke J., Frauenheim T., Elstner M. Effect of Polarization on the Opsin Shift in Rhodopsins. 2. Empirical Polarization Models for Proteins. J. Phys. Chem. B. 2008;112(37):11468–11478. doi: 10.1021/jp802409k
  14. Sekharan S., Sugihara M., Buss V. Origin of Spectral Tuning in Rhodopsin – It Is Not the Binding Pocket. Angewandte Chemie International Edition. 2006;46(1–2):269–271. doi: 10.1002/anie.200603306
  15. Coto P.B., Strambi A., Ferre N., Olivucci M. The color of rhodopsins at the ab initio multiconfigurational perturbation theory resolution. PNAS USA. 2006;103:17154–17159. doi: 10.1073/pnas.0604048103
  16. Wanko M., Hoffmann M., Strodel P., Koslowski A., Thiel W., Neese F., Frauenheim T., Elstner M. Calculating Absorption Shifts for Retinal Proteins: Computational Challenges. J. Phys. Chem. B. 2005;109(8):3606–3615. doi: 10.1021/jp0463060
  17. Wanko M., Hoffmann M., Frauenheim T., Elstner M. Computational photochemistry of retinal proteins. J. Comput. Aided Mol. Des. 2006;20:511–518. doi: 10.1007/s10822-006-9069-8
  18. Birge R.R., Barlow R.B. On the molecular origins of thermal noise in vertebrate and invertebrate photoreceptors. Biophysical Chemistry. 1995;55(1–2):115–126. doi: 10.1016/0301-4622(94)00145-A
  19. Tavan P., Schulten K., Oesterhelt D. The Effect of Protonation and Electrical Interactions on the Stereochemistry of Retinal Schiff Bases. Biophysical Journal. 1985;47(3):415–430. doi: 10.1016/S0006-3495(85)83933-3
  20. Birge R.R., Murray L.P., Pierce B.M., Akita H., Balogh-Nair V., Findsen L.A., Nakanishi K. Two-photon spectroscopy of locked-11-cis-rhodopsin: evidence for a protonated Schiff base in a neutral protein binding site. PNAS USA. 1985;82:4117–4121. doi: 10.1073/pnas.82.12.4117
  21. Matthews G. Dark noise in the outer segment membrane current of green rod photoreceptors from toad retina. The Journal of Physiology. 1984;349(1):607–618. doi: 10.1113/jphysiol.1984.sp015176
  22. Baylor D.A., Matthews G., Yau K.M. Two components of electrical dark noise in toad retinal rod outer segments. The Journal of Physiology. 1980;309(1):591–621. doi: 10.1113/jphysiol.1980.sp013529
  23. Polli D., Altoe P., Weingart O., Spillane K.M., Manzoni C., Brida D., Tomasello G., Orlandi G., Kukura P., Mathies R.A., Garavelli M., Cerullo G. Conical intersection dynamics of the primary photoisomerization event in vision. Nature. 2010;467:440–443. doi: 10.1038/nature09346
  24. Nadtochenko V.A., Smitienko O.A., Feldman T.B., Mozgovaya M.N., Shelaev I.V., Gostev F.E., Sarkisov O.M., Ostrovsky M.A. Conical intersection participation in femtosecond dynamics of visual pigment rhodopsin chromophore cis-trans photoisomerization. Dokl. Biochem. Biophys. 2012;446:242–246. doi: 10.1134/S1607672912050080
  25. Yabushita A., Kobayashi T., Tsuda M. Time-resolved spectroscopy of ultrafast photoisomerization of octopus rhodopsin under photoexcitation. J. Phys. Chem. B. 2012;116:1920–1926. doi: 10.1021/jp209356s
  26. Peteanu L.A., Schoenlein R.W., Wang Q., Mathies R.A., Shank C.V. The first step in vision occurs in femtoseconds: complete blue and red spectral studies. Proc. Natl. Acad. Sci. USA. 1993;90:11762–11766. doi: 10.1073/pnas.90.24.11762
  27. Mizukami T., Kandori H., Shichida Y., Chen A.-H., Derguini F., Caldwell C.G., Biffe C., Nakanishi K., Yoshizawa T. Photoisomerization mechanism of the rhodopsin chromophore: picosecond photolysis of pigment containing 11-cis-locked eight-membered ring retinal. Proc. Natl. Acad. Sci. USA. 1993;90:4072–4076. doi: 10.1073/pnas.90.9.4072
  28. Kandori H., Matuoka S., Shichida Y., Yoshizawa T., Ito M., Tsukida K., Balogh-Nair V., Nakanishi K. Mechanism of isomerisation of rhodopsin studied by use of 11-cis-locked rhodopsin analogues excited with a picoseconds laser pulse. Biochemistry. 1989;28:6460–6467. doi: 10.1021/bi00441a045
  29. Schoenlein R.W., Peteanu L.A., Mathies R.A., Shank C.V. The first step in vision: femtosecond isomerization of rhodopsin. Science. 1991;254:412–415. doi: 10.1126/science.1925597
  30. Dartnall H.J. The photosensitivities of visual pigments in the presence of hydroxylamine. Vision Res. 1968;8:339–358. doi: 10.1016/0042-6989(68)90104-1
  31. Tittor J., Oesterhelt D. The quantum yield of bacteriorhodopsin. FEBS Letters. 1990;263(2):269–273. doi: 10.1016/0014-5793(90)81390-A
  32. Furutani Y., Terakita A., Shichida Y., Kandori H. FTIR Studies of the Photoactivation Processes in Squid Retinochrome. Biochemistry. 2005;44(22):7988–7997. doi: 10.1021/bi050219w
  33. Matsuyama T., Yamashita T., Imamoto Y., Shichida Y. Photochemical Properties of Mammalian Melanopsin. Biochemistry. 2012;51(27):5454–5462. doi: 10.1021/bi3004999
  34. Smitienko O., Nadtochenko V., Feldman T., Balatskaya M., Shelaev I., Gostev F., Sarkisov O., Ostrovsky M. Femtosecond laser spectroscopy of the rhodopsin photochromic reaction: a concept for ultrafast optical molecular switch creation (ultrafast reversible photoreaction of rhodopsin). Molecules. 2014;19:18351–18366. doi: 10.3390/molecules191118351
  35. Yan M., Rothberg L., Callender R. Femtosecond Dynamics of Rhodopsin Photochemistry Probed by a Double Pump Spectroscopic Approach. J. Phys. Chem. B. 2001;105(4):856–859 doi: 10.1021/jp002036j
  36. Bazhenov V., Schmidt P., Atkinson G.H., Nanosecond photolytic interruption of bacteriorhodopsin photocycle: K-590 – BR-570 reaction. Biophysical Journal. 1992;61(6):1630–1637. doi: 10.1016/S0006-3495(92)81966-5
  37. Govindjee R., Balashov S.P., Ebrey T.G. Quantum efficiency of the photochemical cycle of bacteriorhodopsin. Biophys. J. 1990;58:597–608. doi: 10.1016/S0006-3495(90)82403-6
  38. Birge R.R., Cooper T.M., Lawrence A.F., Masthay M.B., Vasilakis C., Zhang C.F., Zidovetzki R. A spectroscopic, photocalorimetric, and theoretical investigation of the quantum efficiency of the primary event in bacteriorhodopsin. J. Am. Chem. Soc. 1989;111(11):4063–4074. doi: 10.1021/ja00193a044
  39. Suzuki T., Callender R.H. Primary photochemistry and photoisomerization of retinal at 77 degrees K in cattle and squid rhodopsins. Biophys. J. 1981;34:261–270. doi: 10.1016/S0006-3495(81)84848-5
  40. Hurley J., Ebrey T., Honig B., Ottolenghi M. Temperature and wavelength effects on the photochemistry of rhodopsin, isorhodopsin, bacteriorhodopsin and their photoproducts. Nature. 1977;270:540–542. doi: 10.1038/270540a0
  41. Kim J.E., Tauber M.E., Mathies R.A. Wavelength Dependent Cis-Trans Isomerization in Vision. Biochemistry. 2001;40(46):13774–13778. doi: 10.1021/bi0116137
  42. Wang Q., Schoenlein R.W, Peteanu L.A., Mathies R.A., Shank C.V. Vibrationally coherent photochemistry in the femtosecond primary event of vision. Science. 1994;266:422–424. doi: 10.1126/science.7939680
  43. Johnson P.J.M., Halpin A., Morizumi T., Prokhorenko V.I., Ernst O.P., Miller R.J.D. Local vibrational coherences drive the primary photochemistry of vision. Nat. Chem. 2015;7:980–986. doi: 10.1038/nchem.2398
  44. Schnedermann C., Liebel M., Kukura P. Mode-specificity of vibrationally coherent internal conversion in rhodopsin during the primary visual event. J. Am. Chem. Soc. 2015;137:2886–2891. doi: 10.1021/ja508941k
  45. Smitienko O.A., Mozgovaya M.N., Shelaev I.V., Gostev F.E., Feldman T.B., Nadtochenko V.A., Sarkisov O.M., Ostrovsky M.A. Femtosecond formation dynamics of primary photoproducts of visual pigment rhodopsin. Biochemistry (Moscow). 2010;75:25–35. doi: 10.1134/S0006297910010049
  46. Worth G.A., Cederbaum L.S. Beyond Born-Oppenheimer: molecular dynamics through a conical intersection. Annu. Rev. Phys. Chem. 2004;55:127–158. doi: 10.1146/annurev.physchem.55.091602.094335
  47. Kochendoerfer G.G., Mathies R.A. Spontaneous emission study of the femtosecond isomerization dynamics of rhodopsin. J. Phys. Chem. 1996;100:14526–14532. doi: 10.1021/jp960509
  48. Doukas A.G., Junnarkar M.R., Alfano R.R., Callender R.H., Kakitani T., Honig B. Fluorescence quantum yield of visual pigments: evidence for subpicosecond isomerization rates. PNAS USA. 1984;81:4790–4794. doi: 10.1073/pnas.81.15.4790
  49. Guzzo A.V., Pool G.L. Visual Pigment Fluorescence. Science. 1968;159(3812):312–314. doi: 10.1126/science.159.3812.312
  50. Polli D., Rivalta I., Nenov A., Weingart O., Garavelli M., Cerullo G. Tracking the primary photoconversion events in rhodopsins by ultrafast optical spectroscopy. Photochem. Photobiol. Sci. 2015;14:213–228. doi: 10.1039/c4pp00370e
  51. Tscherbul T.V., Brumer P. Quantum coherence effects in natural light-induced processes: cis–trans photoisomerization of model retinal under incoherent excitation. Phys. Chem. Chem. Phys. 2015;17:30904–30913. doi: 10.1039/C5CP01388G
  52. Rivalta I., Nenov A., Weingart O., Cerullo G., Garavelli M., Mukamel S. Modelling time-resolved two-dimensional electronic spectroscopy of the primary photoisomerization event in rhodopsin. J. Phys. Chem. B. 2014;118:8396–8405. doi: 10.1021/jp502538m
  53. Warshel A. Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture). Angew. Chem. Int. Ed. Engl. 2014;53(38):10020–10031. doi: 10.1002/anie.201403689
  54. Chung W.C., Nanbu S., Ishida T. QM/MM trajectory surface hopping approach to photoisomerization of rhodopsin and isorhodopsin: the origin of faster and more efficient isomerization for rhodopsin. J. Phys. Chem. B. 2012;116:8009–8023. doi: 10.1021/jp212378u
  55. Weingart O., Garavelli M. Modelling vibrational coherence in the primary rhodopsin photoproduct. J. Chem. Phys. 2012;137:22A523. doi: 10.1063/1.4742814
  56. Schapiro I., Ryazantsev M.N., Frutos L.M., Ferre N., Lindh R., Olivucci M. The ultrafast photoisomerizations of rhodopsin and bathorhodopsin are modulated by bond length alternation and HOOP driven electronic effects. J. Am. Chem. Soc. 2011;133:3354–3364. doi: 10.1021/ja1056196
  57. Weingart O., Altoe P., Stenta M., Bottoni A., Orlandi G., Garavelli M. Product formation in rhodopsin by fast hydrogen motions. Phys. Chem. Chem. Phys. 2011;13:3645–3648. doi: 10.1039/c0cp02496a
  58. Abe M., Ohtsuki Y., Fujimura Y., Domcke W. Optimal control of ultrafast cis-trans photoisomerization of retinal in rhodopsin via a conical intersection. J. Chem. Phys. 2005;123:144508. doi: 10.1063/1.2034488
  59. Gonzalez-Luque R., Garavelli M., Bernardi F., Merchan M., Robb M.A., Olivucci M. Computational evidence in favor of a two-state, two-mode model of the retinal chromophore photoisomerization. Proc. Natl. Acad. Sci. USA. 2000;97:9379–9384. doi: 10.1073/pnas.97.17.9379
  60. Callender R. Resonance raman techniques for photolabile samples: Pump-probe and flow. Methods in Enzymology. 1982;88:625–633. doi: 10.1016/0076-6879(82)88077-4
  61. Yoshizawa T., Shichida Y. Low-temperature spectrophotometry of intermediates of rhodopsin. Methods in Enzymology. 1982;81:333–354. doi: 10.1016/S0076-6879(82)81051-3
  62. Kawamura S., Tokunaga F., Yoshizawa T., Sarai A., Kakitani T. Orientational changes of the transition dipole moment of retinal chromophore on the disk membrane due to the conversion of rhodopsin to bathorhodopsin and to isorhodopsin. Vision Research. 1979;19(8):879–884. doi: 10.1016/0042-6989(79)90021-X
  63. Honig B., Karplus M. Implications of torsional potential of retinal isomers for visual excitation. Nature. 1971;229:558–560. doi: 10.1038/229558a0
  64. Kim J.E., Mathies R.A. Anti-stokes Raman study of vibrational cooling dynamics in the primary photochemistry of rhodopsin. J. Phys. Chem. A. 2002;106:8508–8515. doi: 10.1021/jp021069r
  65. Lin S.W., Groesbeek M., van der Hoef I., Verdegem P., Lugtenburg J., Mathies R.A. Vibrational assignment of torsional normal modes of rhodopsin: probing excited-state isomerization dynamics along the reactive C11=C12 torsion coordinate. J. Phys. Chem. B. 1998;102:2787–2806. doi: 10.1021/jp972752u
  66. Birge R.R. Nature of the primary photochemical events in rhodopsin and bacteriorhodopsin. BBA – Bioenergetics. 1990;1016(3):293–327. doi: 10.1016/0005-2728(90)90163-X
  67. Loppnow G., Mathies R. Excited-state structure and isomerization dynamics of the retinal chromophore in rhodopsin from resonance Raman intensities. Biophysical Journal. 1988;54:35–43. doi: 10.1016/S0006-3495(88)82928-X
  68. Palings I., Van den Berg E.M.M., Lugtenburg J., Mathies R.A. Complete assignment of the hydrogen out-of-plane wagging vibrations of bathorhodopsin: chromophore structure and energy storage in the primary photoproduct of vision. Biochemistry. 1989;28(4):1498–1507. doi: 10.1021/bi00430a012
  69. Eyring G., Mathies R.A. Resonance Raman studies of bathorhodopsin: Evidence for a protonated Schiff base linkage. PNAS USA. 1979;76:33–37. doi: 10.1073/pnas.76.1.33
  70. Röhrig U.F., Guidoni L., Laio A., Frank I., Rothlisberger U. A Molecular Spring for Vision. J. Am. Chem. Soc. 2004;126:15328–15329. doi: 10.1021/ja048265r
  71. Nakamichi H., Okada T. Local peptide movement in the photoreaction intermediate of rhodopsin. PNAS USA. 2006;103:12729–12734. doi: 10.1073/pnas.0601765103
  72. Okada T., Le Trong I., Fox B.A., Behnke C.A., Stenkamp R.E., Palczewski K. X-Ray Diffraction Analysis of Three-Dimensional Crystals of Bovine Rhodopsin. Journal of Structural Biology. 2000;130(1):73-80. doi: 10.1006/jsbi.1999.4209
  73. Nakamichi H., Okada T. Crystallographic analysis of primary visual photochemistry. Angew. Chem. Int. Ed. 2006;45:4270–4273. doi: 10.1002/anie.200600595
  74. Palczewski K., Kumasaka T., Hori T., Behnke C.A., Motoshima H., Fox B.A., Trong I.L., Teller D.C., Okada T., Stenkamp R.E., Yamamoto M., Miyano M. Crystal structure of rhodopsin: a G protein-coupled receptor. Science. 2000;289:739–745. doi: 10.1126/science.289.5480.739
  75. Cooper A. Energy uptake in the first step of visual excitation. Nature. 1979;282:531–533. doi: 10.1038/282531a0
  76. Nishioku Y., Nakagawa M., Tsuda M., Terazima M. Energetics and Volume Changes of the Intermediates in the Photolysis of Octopus Rhodopsin at a Physiological Temperature. Biophysical Journal. 2002;83:1136–1146. doi: 10.1016/S0006-3495(02)75237-5
  77. Sekharan S., Morokuma K. Why 11-cis-Retinal? Why Not 7-cis-, 9-cis-, or 13-cis-Retinal in the Eye? J. Am. Chem. Soc. 2011;133(47):19052–19055. doi: 10.1021/ja208789h
  78. Li X., Chung L.W., Morokuma K. Photodynamics of All-trans Retinal Protonated Schiff Base in Bacteriorhodopsin and Methanol Solution. J. Chem. Theory Comput. 2011;7:2694–2698. doi: 10.1021/ct200549z
  79. Hayashi S., Tajkhorshid E., Schulten K. Photochemical Reaction Dynamics of the Primary Event of Vision Studied by Means of a Hybrid Molecular Simulation. Biophysical Journal. 2009;96(2):403–416. doi: 10.1016/j.bpj.2008.09.049
  80. Strambi A., Coto P.B., Frutos L.M., Ferre N., Olivucci M. Relationship between the Excited State Relaxation Paths of Rhodopsin and Isorhodopsin. J. Am. Chem. Soc. 2008;130:3382–3388. doi: 10.1021/ja0749082
  81. Frutos L.M., Andruniow T., Santoro F., Olivucci M. Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry. PNAS USA. 2007;104:7764–7769. doi: 10.1073/pnas.0701732104
  82. Sugihara M., Hufen J., Buss V. Origin and Consequences of Steric Strain in the Rhodopsin Binding Pocket. Biochemistry. 2006;45:801–810. doi: 10.1021/bi0515624
  83. Gascon J.A., Sproviero E.M., Batista V.S. Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin. Acc. Chem. Res. 2006;39:184–193. doi: 10.1021/ar050027t
  84. Garavelli M. Computational Organic Photochemistry: Strategy, Achievements and Perspectives. Theor. Chem. Acc. 2006;116:87–105. doi: 10.1007/s00214-005-0030-z
  85. Cembran A., Bernardi F., Olivucci M., Garavelli M. The retinal chromophore/chloride ion pair: Structure of the photoisomerization path and interplay of charge transfer and covalent states. PNAS USA. 2005;102:6255–6260. doi: 10.1073/pnas.0408723102
  86. Cembran A., Bernardi F., Olivucci M., Garavelli M. Counterion Controlled Photoisomerization of Retinal Chromophore Models: a Computational Investigation. J. Am. Chem. Soc. 2004;126:16018–16037. doi: 10.1021/ja048782+
  87. Gascon J.A., Batista V.S. QM/MM Study of Energy Storage and Molecular Rearrangements Due to the Primary Event in Vision. Biophysical Journal. 2004;87(5):2931–2941. doi: 10.1529/biophysj.104.048264
  88. Hayashi S., Tajkhorshid E., Schulten K. Molecular Dynamics Simulation of Bacteriorhodopsin's Photoisomerization Using Ab Initio Forces for the Excited Chromophore. Biophysical Journal. 2003;85(3):1440–1449. doi: 10.1016/S0006-3495(03)74576-7
  89. Warshel A., Chu Z.T. Nature of the Surface Crossing Process in Bacteriorhodopsin: Computer Simulations of the Quantum Dynamics of the Primary Photochemical Event. J. Phys. Chem. B. 2001;105:9857–9871. doi: 10.1021/jp010704a
  90. Hahn S., Stock G. Quantum-Mechanical Modeling of the Femtosecond Isomerization in Rhodopsin. J. Phys. Chem. B. 2000;104:1146–1149. doi: 10.1021/jp992939g
  91. Yoshizawa T., Kito Y. Chemistry of the Rhodopsin Cycle. Nature. 1958;182:1604–1605. doi: 10.1038/1821604a0
  92. Yoshizawa T., Wald G. Pre-Lumirhodopsin and the Bleaching of Visual Pigments. Nature. 1963;197:1279–1286. doi: 10.1038/1971279a0
  93. Hug S.J., Lewis J.W., Einterz C.M., Thorgeirsson T.E., Kliger D.S. Nanosecond photolysis of rhodopsin: evidence for a new blue-shifted intermediate. Biochemistry. 1990;29:1475–1485. doi: 10.1021/bi00458a019
  94. Busch G.E., Applebury M.L., Lamola A.A., Rentzepis P.M. Formation and Decay of Prelumirhodopsin at Room Temperatures. PNAS USA. 1972;69:2802–2806. doi: 10.1073/pnas.69.10.2802
  95. Peters K., Applebury M.L., Rentzepis P.M. Primary photochemical event in vision: proton translocation. PNAS USA. 1977;74:3119–3123. doi: 10.1073/pnas.74.8.3119
  96. Fukada Y., Shichida Y., Yoshizawa T., Ito M., Kodama A., Tsukida K. Studies on structure and function of rhodopsin by use of cyclopentatrienylidene 11-cis-locked-rhodopsin. Biochemistry. 1984;23:5826–5832. doi: 10.1021/bi00319a023
  97. Buchert J., Stefancic V., Doukas A.G., Alfano R.R., Callender R.H., Pande J., Akita H., Balogh-Nair V., Nakanishi K. Picosecond kinetic absorption and fluorescence studies of bovine rhodopsin with a fixed 11-ene. Biophys. J. 1983;43:279–283. doi: 10.1016/S0006-3495(83)84351-3
  98. Mao B., Tsuda M., Ebrey T.G., Akita H., Balogh-Nair V., Nakanishi K. Flash photolysis and low temperature photochemistry of bovine rhodopsin with a fixed 11-ene. Biophys. J. 1981;35:543–546. doi: 10.1016/S0006-3495(81)84809-6
  99. Levine B.G., Martinez T.M. Isomerization through conical intersections. Annu. Rev. Phys. Chem. 2007;58:613–634. doi: 10.1146/annurev.physchem.57.032905.104612
  100. Hahn S., Stock G. Femtosecond secondary emission arising from the nonadiabatic photoisomerization in rhodopsin. Chemical Physics. 2000;259(2–3):297–312. doi: 10.1016/S0301-0104(00)00201-9
  101. Hahn S., Stock G. Ultrafast cis-trans photoswitching: A model study. J. Chem. Phys. 2002;116:1085–1091. doi: 10.1063/1.1428344
  102. Liu R.S., Yang L.Y., Liu J. Mechanisms of photoisomerization of polyenes in confined media: from organic glasses to protein binding cavities. Photochem. Photobiol. 2007;83:2–10. doi: 10.1562/2006-01-27-RA-786
  103. Kukura P., McCamant D.W., Yoon S., Wandschneider D.B., Mathies R.A. Structural Observation of the Primary Isomerization in Vision with Femtosecond-Stimulated Raman. Science. 2005;310(5750):1006–1009. doi: 10.1126/science.1118379
  104. Lemaitre V., Yeagle P., Watts A. Molecular dynamics simulations of retinal in rhodopsin: from the dark-adapted state towards lumirhodopsin. Biochemistry. 2005;44:12667–12680. doi: 10.1021/bi0506019
  105. Andruniow T., Ferre N., Olivucci M. Structure, initial excited-state relaxation, and energy storage of rhodopsin resolved at the multiconfigurational perturbation theory level. PNAS USA. 2004;101:17908–17913. doi: 10.1073/pnas.0407997101
  106. Borhan B., Soutu M.L., Imai H., Shichida Y., Nakanishi K. Movement of retinal along the visual transduction path. Science. 2000;288:2209–2212. doi: 10.1126/science.288.5474.2209
  107. Liu R.S.H. Photoisomerization by hula-twist: a fundamental supramolecular photochemical reaction. Acc. Chem. Res. 2001;34:555–562. doi: 10.1021/ar000165c
  108. Smith S.O., Courtin J., de Groot H.J.M., Gebhard M., Lugtenburg J. 13C magic-angle spinning NMR studies of bathorhodopsin, the primary photoproduct of rhodopsin. Biochemistry. 1991;30:7409–7415. doi: 10.1021/bi00244a007
  109. Isin B., Schulten K., Tajkhorshid E., Bahar I. Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes. Biophys. J. 2008;95:789–803. doi: 10.1529/biophysj.107.120691
  110. Yamada A., Yamato T., Kakitani T., Yamamoto S. Torsion potential works in rhodopsin. Photochem. Photobiol. 2007;79:476–486. doi: 10.1111/j.1751-1097.2004.tb00037.x
  111. Kholmurodov Kh.T., Feldman T.B., Ostrovsky M.A. Visual pigment rhodopsin: molecular dynamics of 11-cis-retinal chromophore and amino-acid residues in the chromophore center. Computer simulation study, Mendeleev Comm. 2006;1:1–8. doi: 10.1070/MC2006v016n01ABEH002255
  112. Saam J., Tajkhorshid E., Hayashi S., Schulten K. Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin. Biophys. J. 2002;83:3097–3112. doi: 10.1016/S0006-3495(02)75314-9
  113. Ganter U.M., Schmid E.D., Perez-Sala D., Rando R.R., Siebert F. Removal of the 9-methyl group of retinal inhibits signal transduction in the visual process. A Fourier transform infrared and biochemical investigation. Biochemistry. 1989;28:5954–5962. doi: 10.1021/bi00440a036
  114. Han M., Groesbeek M., Smith S.O., Sakmar T.P. Role of the C9 methyl group in rhodopsin activation: characterization of mutant opsins with the artificial chromophore 11-cis-9-demethylretinal. Biochemistry. 1998;37:538–545. doi: 10.1021/bi972060w
  115. Meyer C.K., Bohme M., Ockenfels A., Gartner W., Hofmann K.P, Ernst O.P. Signaling states of rhodopsin. Retinal provides a scaffold for activating proton transfer switches. J. Biol. Chem. 2000;275:19713–19718. doi: 10.1074/jbc.M000603200
  116. Kochendoerfer G.G., Verdegem P.J.E., van der Hoef I., Lugtenburg J., Mathies R.A. Retinal Analog Study of the Role of Steric Interactions in the Excited State Isomerization Dynamics of Rhodopsin. Biochemistry. 1996;35:16230–16240. doi: 10.1021/bi961951l
  117. Lakhno V.D., Shigaev A.S., Feldman T.B., Ostrovsky M.A., Nadtochenko V.A. Quantum-classical model of retinal photoisomerization reaction in visual pigment rhodopsin. Doklady Biochemistry and Biophysics. 2016;471(1):435-439. doi: 10.1134/S1607672916060168
  118. Shigaev A.S., Feldman T.B., Nadtochenko V.A., Ostrovsky M.A., Lakhno V.D. Investigation of Rhodopsin Chromophore Photoisomerization Based on the Quantum-Classical Model. Mathematical Biology and Bioinformatics. 2018;13(1):169–186 (in Russ.). doi: 10.17537/2018.13.169
  119. Shigaev A.S., Feldman T.B., Nadtochenko V.A., Ostrovsky M.A., Lakhno V.D. Quantum-classical modeling of rhodopsin photoisomerization: Keldysh Institute Preprints. 2018. № 27. doi: 10.20948/prepr-2018-27-e
  120. Shigaev A.S., Feldman T.B., Nadtochenko V.A., Ostrovsky M.A., Lakhno V.D. Quantum-classical model of the rhodopsin retinal chromophore cis–trans photoisomerization with modified inter-subsystem coupling. Computational and Theoretical Chemistry. 2020;1181. Article No. 112831. doi: 10.1016/j.comptc.2020.112831
  121. Holstein T. Studies of polaron motion: Part I. The molecular-crystal model. Ann. Phys. 1959;8:325–342. doi: 10.1016/0003-4916(59)90002-8
  122. Davydov A.S. The theory of contraction of proteins under their excitation. J. Theor. Biology. 1973;38:559–569. doi: 10.1016/0022-5193(73)90256-7
  123. Davydov A.S. Solitons and energy transfer along protein molecules. J. Theor. Biology. 1977;66:379–387. doi: 10.1016/0022-5193(77)90178-3
  124. Physics in One Dimension. Ed. Bernassoni J. Springer-Verlag, 1981. (Springer series in solid-state sciences. Vol. 23). ISBN: 978-3-642-81592-8.
  125. Okahata Y., Kobayashi T., Tanaka K., Shimomura M.J. Anisotropic Electric Conductivity in an Aligned DNA Cast Film. J. Am. Chem. Soc. 1998;120:6165–6166. doi: 10.1021/ja980165w
  126. Modern Methods for Theoretical Physical Chemistry of Biopolymers. Eds. Starikov E.B., Lewis J.P., Tanaka S. Elsevier, 2006. ISBN: 9780080461014.
  127. Cramer T., Steinbrecher T., Labahn A., Koslowski T. Static and dynamic aspects of DNA charge transfer: a theoretical perspective. Phys. Chem. Chem. Phys. 2005;7:4039–4050. doi: 10.1039/b507454a
  128. Lakhno V.D. Oscilations in the primary charge separation in bacterial photosynthesis. Phys. Chem. Chem. Phys. 2002;4:2246–2250. doi: 10.1039/b102700j
  129. Lakhno V.D. Dynamical theory of primary processes of charge separation in the photosynthetic reaction center. J. Biol. Phys. 2005;31:145–159. doi: 10.1007/s10867-005-5109-1
  130. Komineas S., Kalosakas G., Bishop A.R. Effects of intrinsic base-pair fluctuations on charge transport in DNA. Phys. Rev. E. 2002;65:061905. doi: 10.1103/PhysRevE.65.061905
  131. Maniadis P., Kalosakas G., Rasmussen K.O., Bishop A.R. AC conductivity in a DNA charge transport model. Phys. Rev. E. 2005;72:021912. doi: 10.1103/PhysRevE.72.021912
  132. Diaz E., Lima R.P.A., Dominguez-Adame F. Bloch-like oscillations in the Peyrard-Bishop-Holstein model. Phys. Rev. B. 2008;78:134303. doi: 10.1103/PhysRevB.78.134303
  133. Lakhno V.D., Sultanov V.B., Montgomery Pettitt B. Combined hopping–superexchange model of a hole transfer in DNA. Chem. Phys. Lett. 2004;400:47–53. doi: 10.1016/j.cplett.2004.10.077
  134. Shigaev A.S., Ponomarev O.A., Lakhno V.D. A new approach to microscopic modeling of a hole transfer in heteropolymer DNA. Chem. Phys. Lett. 2011;513:276–279. doi: 10.1016/j.cplett.2011.07.080
  135. Korshunova A.N., Lakhno V.D. A new type of localized fast moving electronic excitations in molecular chains. Physica E. 2014;60:206–209. doi: 10.1016/j.physe.2014.02.025
  136. Fialko N.S., Lakhno V.D. Nonlinear dynamics of excitations in DNA. Phys. Lett. A. 2000;278:108–112. doi: 10.1016/S0375-9601(00)00755-6
  137. Liu J., Liu M.Y., Nguyen J.B., Bhagat A., Mooney V., Yan E.C.Y. Thermal Decay of Rhodopsin: Role of Hydrogen Bonds in Thermal Isomerization of 11-cis Retinal in the Binding Site and Hydrolysis of Protonated Schiff Base. J. Am. Chem. Soc. 2009;131:8750–8751. doi: 10.1021/ja903154u
  138. Okada T., Sugihara M., Bondar A.-N., Elstner M., Entel P., Buss V. The Retinal Conformation and its Environment in Rhodopsin in Light of a New 2.2A Crystal Structure. Journal of Molecular Biology. 2004;342(2):571–583. doi: 10.1016/j.jmb.2004.07.044
  139. Palczewski K., Kumasaka T., Hori T., Behnke C.A., Motoshima H., Fox B.A., Le Trong I., Teller D.C., Okada T., Stenkamp R.E., Yamamoto M., Miyano M. Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor. Science. 2000;289(5480):739–745. doi: 10.1126/science.289.5480.739
  140. Nagata T., Terakita A., Kandori H., Shichida Y., Maeda A. The Hydrogen-Bonding Network of Water Molecules and the Peptide Backbone in the Region Connecting Asp83, Gly120, and Glu113 in Bovine Rhodopsin. Biochemistry. 1998;37:17216–17222. doi: 10.1021/bi9810149
  141. Nagata T., Terakita A., Kandori H., Kojima D., Shichida Y., Maeda A. Water and Peptide Backbone Structure in the Active Center of Bovine Rhodopsin. Biochemistry. 1997;36:6164–6170. doi: 10.1021/bi962920t
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Шигаев А.С., Лихачёв И.В., Лахно В.Д. Проблемы квантово-классического моделирования первичной фотореакции в родопсине. Математическая биология и биоинформатика. 2022;17(2):360-385. doi: 10.17537/2022.17.360
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