TCB Publications - Abstract

Ilya Logunov, William Humphrey, Klaus Schulten, and Mordechai Sheves. Molecular dynamics study of the 13-cis form (bR548) of bacteriorhodopsin and its photocycle. Biophysical Journal, 68:1270-1282, 1995. (PMC: 1282023)

LOGU95C The structure and the photocycle of bacteriorhodopsin (bR) containing 13-cis, 15-/it syn retinal, so-called $bR_{548}$, has been studied by means of molecular dynamics simulations performed on the complete protein. The simulated structure of $bR_{548}$ was obtained through isomerization of in situ retinal around both its $C_{13}-C_{14} $ and its $C_{15}-N$ bond starting from the simulated structure of $bR_{568}$ described previously, containing all-trans, 15-anti retinal. After a 50-ps equilibration, the resulting structure of $bR_{548}$ was examined by replacing retinal by analogues with modified $\beta$-ionone rings and comparing with respective observations. The photocycle of $bR_{548}$ was simulated by inducing a rapid 13-cis, 15-anti $\rightarrow$ all- trans, 15-syn isomerization through a 1-ps application of a potential that destabilizes the 13-cis isomer. The simulation resulted in structures consistent with the J, K, and L intermediates observed in the photocycle of $bR_{548}$. The results offer an explanation of why an unprotonated retinal Schiff base points to the intracellular rather than to the extracellular site. The simulations suggest also that leakage from the $bR_{548}$ to the $bR_{568}$ cycle arises due to an initial 13-cis, 15-anti ($\rightarrow$) all-trans, 15-anti photoisomerization.

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