A. S. Shigaev, T. B. Feldman, V. A. Nadtochenko, M. A. Ostrovsky, V. D. Lakhno
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Список литературы
|
|
|
1. |
Lamb T. D., Collin S. P., Pugh E. N. Jr., “Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup”, Nat. Rev. Neurosci., 8 (2007), 960–976 |
2. |
Menon S. T., Han M., Sakmar T. P., “Rhodopsin: Structural Basis of Molecular Physiology”, Physiol. Rev., 81 (2001), 1659–1688 |
3. |
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., 16 (2000), 365–392 |
4. |
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., 446 (2012), 242–246 |
5. |
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, 467 (2010), 440–443 |
6. |
Yabushita A., Kobayashi T., Tsuda M., “Time-resolved spectroscopy of ultrafast photoisomerization of octopus rhodopsin under photoexcitation”, J. Phys. Chem. B, 116 (2012), 1920–1926 |
7. |
Dartnall H. J., “The photosensitivities of visual pigments in the presence of hydroxylamine”, Vision Res., 8 (1968), 339–358 |
8. |
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, 28 (1989), 6460–6467, PMID: 2790007 |
9. |
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-cislocked eight-membered ring retinal”, Proc. Natl. Acad. Sci. USA, 90 (1993), 4072–4076 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC46448 |
10. |
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, 90 (1993), 11762–11766 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC48064/ |
11. |
Schoenlein R. W., Peteanu L. A., Mathies R. A., Shank C. V., “The first step in vision: femtosecond isomerization of rhodopsin”, Science, 254 (1991), 412–415 |
12. |
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., 7 (2015), 980–986 |
13. |
Schnedermann C., Liebel M., Kukura P., “Mode-specificity of vibrationally coherent internal conversion in rhodopsin during the primary visual event”, J. Am. Chem. Soc., 137 (2015), 2886–2891 |
14. |
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, 19 (2014), 18351–18366 |
15. |
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), 75 (2010), 25–35 |
16. |
Worth G. A., Cederbaum L. S., “Beyond Born-Oppenheimer: molecular dynamics through a conical intersection”, Annu. Rev. Phys. Chem., 55 (2004), 127–158 |
17. |
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, 97 (2000), 9379–9384 http://www.pnas.org/content/97/17/9379 |
18. |
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., 14 (2015), 213–228 |
19. |
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., 133 (2011), 3354–3364 |
20. |
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., 123 (2015), 144508 |
21. |
Levine B. G., Martinez T. M., “Isomerization through conical intersections”, Annu. Rev. Phys. Chem., 58 (2008), 613–634 |
22. |
Tomasello G., Olaso-Gonzalez G., Altoe P., Stenta M., Serrano-Andres L., Merchan 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., 131 (2009), 5172–5186 |
23. |
Kochendoerfer G. G., Mathies R. A., “Spontaneous emission study of the femtosecond isomerization dynamics of rhodopsin”, J. Phys. Chem., 100 (1996), 14526–14532 https://pdfs.semanticscholar.org/9dc8/cae3a9c373c13a4bb434a1fb53a9eb82b411.pdf |
24. |
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, 116 (2012), 8009–8023 |
25. |
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, 118 (2014), 8396–8405 |
26. |
Tscherbul T. V., Brumer P., “Quantum coherence effects in natural lightinduced processes: cis-trans photoisomerization of model retinal under incoherent excitation”, Phys. Chem. Chem. Phys., 17 (2015), 30904–30913 |
27. |
Weingart O., Altoe P., Stenta M., Bottoni A., Orlandi G., Garavelli M., “Product formation in rhodopsin by fast hydrogen motions”, Phys. Chem. Chem. Phys., 13 (2011), 3645–3648 |
28. |
Weingart O., Garavelli M., “Modelling vibrational coherence in the primary rhodopsin photoproduct”, J. Chem. Phys., 137 (2012), 22A523 |
29. |
Honig B., Karplus M., “Implications of torsional potential of retinal isomers for visual excitation”, Nature, 229 (1971), 558–560, PMID: 4925351 |
30. |
Warshel A., “Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines”, The Nobel Prizes: Nobel Lecture, 8 December 2013, 159 https://pdfs.semanticscholar.org/c2f4/d2c43964731d99ae76da4e6a5cc0702abb71.pdf |
31. |
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, 101 (2004), 17908–17913 |
32. |
Borhan B., Soutu M. L., Imai H., Shichida Y., Nakanishi K., “Movement of retinal along the visual transduction path”, Science, 288 (2000), 2209–2212 |
33. |
Liu R. S. H., “Photoisomerization by hula-twist: a fundamental supramolecular photochemical reaction”, Acc. Chem. Res., 34 (2001), 555–562 |
34. |
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., 83 (2007), 2–10 |
35. |
Nakamichi H., Okada T., “Crystallographic analysis of primary visual photochemistry”, Angew. Chem. Int. Ed., 45 (2006), 4270–4273 |
36. |
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, 30 (1991), 7409–7415 |
37. |
Saam J., Tajkhorshid E., Hayashi S., Schulten K., “Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin”, Biophys. J., 83 (2002), 3097–3112 |
38. |
Yamada A., Yamato T., Kakitani T., Yamamoto S., “Torsion potential works in rhodopsin”, Photochem. Photobiol., 79 (2014), 476–486 |
39. |
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., 1 (2006), 1–8 |
40. |
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., 95 (2008), 789–803 |
41. |
Smith J. C., Roux B., “Eppur si muove! The 2013 nobel prize in chemistry”, Structure, 21 (2013), 2102–2105 |
42. |
Holstein T., “Studies of polaron motion: Part I. The molecular-crystal model”, Ann. Phys., 8 (1959), 325–342 |
43. |
Davydov A. S., “The theory of contraction of proteins under their excitation”, J. Theor. Biology, 38 (1973), 559–569 |
44. |
Davydov A. S., “Solitons and energy transfer along protein molecules”, J. Theor. Biology, 66 (1977), 379–387 |
45. |
Bernassoni J. (ed.), Physics in one dimension. Springer series in solid-state sciences, Springer-Verlag, 1981 |
46. |
Okahata Y., Kobayashi T., Tanaka K., Shimomura M. J., “Anisotropic Electric Conductivity in an Aligned DNA Cast Film”, J. Am. Chem. Soc., 120 (1998), 6165–6166 |
47. |
Starikov E. B., Tanaka S., Lewis J. P. (eds.), Modern Methods for Theoretical Physical Chemistry of Biopolymers, Elsevier, 2006 |
48. |
Cramer T., Steinbrecher T., Labahn A., Koslowski T., “Static and dynamic aspects of DNA charge transfer: a theoretical perspective”, Phys. Chem. Chem. Phys., 7 (2005), 4039–4050 |
49. |
Lakhno V. D., “Oscilations in the primary charge separation in bacterial photosynthesis”, Phys. Chem. Chem. Phys., 4 (2002), 2246–2250 |
50. |
Lakhno V. D., “Dynamical theory of primary processes of charge separation in the photosynthetic reaction center”, J. Biol. Phys., 31 (2005), 145–159 |
51. |
Komineas S., Kalosakas G., Bishop A. R., “Effects of intrinsic base-pair fluctuations on charge transport in DNA”, Phys. Rev. E, 65 (2002), 061905 |
52. |
Maniadis P., Kalosakas G., Rasmussen K. O., Bishop A. R., “Ac conductivity in a DNA charge transport model”, Phys. Rev. E, 72 (2005), 021912 |
53. |
Diaz E., Lima R. P. A., Dominguez-Adame F., “Bloch-like oscillations in the Peyrard-Bishop-Holstein model”, Phys. Rev. B, 78 (2008), 134303 |
54. |
Lakhno V. D., Sultanov V. B., Montgomery Pettitt B., “Combined hopping-superexchange model of a hole transfer in DNA”, Chem. Phys. Lett., 400 (2004), 47–53 |
55. |
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., 513 (2011), 276–279 |
56. |
Korshunova A. N., Lakhno V. D., “A new type of localized fast moving electronic excitations in molecular chains”, Physica E, 60 (2014), 206–209 |
57. |
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, 28 (1989), 5954–5962, PMID: 2505843 |
58. |
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, 37 (1998), 538–545 |
59. |
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., 275 (2000), 19713–19718 |
60. |
Lemaitre V., Yeagle P., Watts A., “Molecular dynamics simulations of retinal in rhodopsin: from the dark-adapted state towards lumirhodopsin”, Biochemistry, 44 (2005), 12667–12680 |
61. |
Kholmurodov Kh. T., Feldman T. B., Ostrovskii M. A., “Molecular Simulation Studies in Material and Biological Sciences”, Molecular dynamics simulation and experimental studies of the visual pigment rhodopsin: multiple conformational states and structural changes, ed. Kh.T. Kholmurodov, Nova Science Publishers Inc., N.Y., 2007, 85–113 |
62. |
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 C11dC12 torsion coordinate”, J. Phys. Chem. B, 102 (1998), 2787–2806 |
63. |
Kim J. E., Mathies R. A., “Anti-stokes Raman study of vibrational cooling dynamics in the primary photochemistry of rhodopsin”, J. Phys. Chem. A, 106 (2002), 8508–8515 |
64. |
Fialko N. S., Lakhno V. D., “Nonlinear dynamics of excitations in DNA”, Phys. Lett. A, 278 (2000), 108–112 |
65. |
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, 266 (1994), 422–424 |
66. |
Feldman T. B., Smitienko O. A., Shelaev I. V., Gostev F. E., Nekrasova O. V., Dolgikh D. A., Nadtochenko V. A., Kirpichnikov M. P., Ostrovsky M. A., “Femtosecond spectroscopic study of photochromic reactions of bacteriorhodopsin and visual rhodopsin”, J. Photochem. Photobiol. B: Biology, 164 (2016), 296–305 |