Key role of active-site water molecules in bacteriorhodopsin proton-transfer reactions.
作者： Ana-Nicoleta Bondar , Jerome Baudry , Sándor Suhai , Stefan Fischer , Jeremy C. Smith
DOI: 10.1021/JP801916F
关键词:
摘要: The functional mechanism of the light-driven proton pump protein bacteriorhodopsin depends on location water molecules in active site at various stages photocycle and their roles proton-transfer steps. Here, free energy computations indicate that electrostatic interactions favor presence a cytoplasmic-side molecule hydrogen bonding to retinal Schiff base state preceding transfer from Asp85. However, nonequilibrium nature pumping process means probability occupancy given both energies insertion this other sites during steps kinetic accessibility these time scale reaction has dramatic effect transfer: is channeled Thr89 side retinal, whereas trans...
acs.org
sci-hub.se 参考文章(96)
Joel E. Morgan, Ahmet S. Vakkasoglu, Robert B. Gennis, Akio Maeda, Water Structural Changes in the L and M Photocycle Intermediates of Bacteriorhodopsin as Revealed by Time-Resolved Step-Scan Fourier Transform Infrared (FTIR) Spectroscopy† Biochemistry. ,vol. 46, pp. 2787- 2796 ,(2007) , 10.1021/BI0616596
H. Otto, T. Marti, M. Holz, T. Mogi, L. J. Stern, F. Engel, H. G. Khorana, M. P. Heyn, Substitution of amino acids Asp-85, Asp-212, and Arg-82 in bacteriorhodopsin affects the proton release phase of the pump and the pK of the Schiff base. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 87, pp. 1018- 1022 ,(1990) , 10.1073/PNAS.87.3.1018
Shigehiko Hayashi, Iwao Ohmine, Proton Transfer in Bacteriorhodopsin: Structure, Excitation, IR Spectra, and Potential Energy Surface Analyses by an ab Initio QM/MM Method Journal of Physical Chemistry B. ,vol. 104, pp. 10678- 10691 ,(2000) , 10.1021/JP001508R
Sergei Grudinin, Georg Büldt, Valentin Gordeliy, Artur Baumgaertner, Water molecules and hydrogen-bonded networks in bacteriorhodopsin--molecular dynamics simulations of the ground state and the M-intermediate. Biophysical Journal. ,vol. 88, pp. 3252- 3261 ,(2005) , 10.1529/BIOPHYSJ.104.047993
Ana-Nicoleta Bondar, Stefan Fischer, Jeremy C. Smith, Marcus Elstner, Sándor Suhai, Key Role of Electrostatic Interactions in Bacteriorhodopsin Proton Transfer Journal of the American Chemical Society. ,vol. 126, pp. 14668- 14677 ,(2004) , 10.1021/JA047982I
Arieh Warshel, Conversion of light energy to electrostatic energy in the proton pump of Halobacterium halobium. Photochemistry and Photobiology. ,vol. 30, pp. 285- 290 ,(1979) , 10.1111/J.1751-1097.1979.TB07148.X
Janos K Lanyi, Brigitte Schobert, Crystallographic structure of the retinal and the protein after deprotonation of the Schiff base: the switch in the bacteriorhodopsin photocycle. Journal of Molecular Biology. ,vol. 321, pp. 727- 737 ,(2002) , 10.1016/S0022-2836(02)00682-4
Benoît Roux, The calculation of the potential of mean force using computer simulations Computer Physics Communications. ,vol. 91, pp. 275- 282 ,(1995) , 10.1016/0010-4655(95)00053-I
Janos K Lanyi, Brigitte Schobert, Mechanism of Proton Transport in Bacteriorhodopsin from Crystallographic Structures of the K, L, M1, M2, and M2′ Intermediates of the Photocycle Journal of Molecular Biology. ,vol. 328, pp. 439- 450 ,(2003) , 10.1016/S0022-2836(03)00263-8
Ana-Nicoleta Bondar, Jeremy C. Smith, Stefan Fischer, Structural and energetic determinants of primary proton transfer in bacteriorhodopsin Photochemical and Photobiological Sciences. ,vol. 5, pp. 547- 552 ,(2006) , 10.1039/B516451F