QM/MM investigation of the hydrogen-bonding interactions in putative K and early-M intermediates of the bacteriorhodopsin photocycle

Author： Bondar A. N. Smith J. C. Fischer S. K.

Publisher： Taylor & Francis Ltd

ISSN： 0141-1594

Source： Phase Transitions: A Multinational Journal, Vol.78, Iss.9-11, 2005-09, pp. : 671-675

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Abstract

The light-driven photocycle of the bacteriorhodopsin proton pump contains several intermediate states characterized by their spectroscopic signals. Numerous experimental investigations, including high-resolution X-ray crystallography, have provided valuable insight into the nature and the extent of the structural rearrangements along the photocycle. Nevertheless, the detailed hydrogen-bonding interactions of the retinal Schiff base and of the groups involved in proton transfer remain under debate. Combined Quantum Mechanical/Molecular Mechanical (QM/MM) calculations are employed here to assess the hydrogen-bonding interactions in the retinal binding pocket of putative K and early-M stable structures. In both of the starting coordinate sets the retinal chain is highly twisted, with the Schiff base pointing towards the extracellular side of the membrane. The optimization of either the K or the early-M state structure by considering the Schiff base protonated and Asp85 negatively charged (i.e., as in the K intermediate) preserves the highly twisted configuration of the retinal chain. In the case where the optimizations are performed with neutral Schiff base and neutral Asp85 (i.e., as in the M intermediate) the chromophore relaxes and the Schiff base orients towards the cytoplasm. The twisted retinal configuration with the deprotonated Schiff base pointing towards the extracellular side of the membrane is found to be unstable.