Molecular Dynamics Study of the Nature and Origin of the Twisted Structure of the Retinal Chromophore in Bacteriorhodopsin

Emadeddin Tajkhorshid, Jérôme Baudry, Klaus Schulten and Sándor Suhai

Abstract

The results from crystallographic studies and theoretical ab initio calculations of the retinal Schiff base have shown that the molecule has a banana-shaped planar structure in the isolated form as well as in solution. Experimental studies, however, suggest that the retinal chromophore adopts a twisted structure when positioned in its binding pocket in bacteriorhodopsin (bR). The position and extent of this twist has been reported to be important with respect to the pK_a of the chromophore. The dark adaptation of the pigment and the last step of the bR photocycle imply low barriers against the rotation of the double bonds in the Schiff base region. In the present study, using molecular dynamics simulation techniques and applying a recently developed set of parameters for the retinal Schiff base, we have examined the planarity of the main polyene chain of the retinal chromophore in bR. The largest deviations from a planar structure are, interestingly, observed for the C₁₃=C₁₄ and C₁₅=N₁₆ double bonds in the retinal Schiff base structure. The rest of the torsional angles, although having lower torsional barriers in some cases, do not significantly deviate from the planar structure. The results of the simulations of different mutants of the pigment show that, among the studied amino acids of the binding pocket, Trp₈₆ side chain has the largest impact on the planarity of the chromophore, and in the W86A mutant form of the pigment the retinal is almost planar. According to our MD simulations, deletion of the methyl substituent on C₁₃ (C₂₀), removing the water molecule hydrogen bonded to H₁₅, or mutation of other amino acids to alanine did not show any significant influence with respect to the planarity of the chromophore. The results from the present study indicate the importance of the bulky residue of Trp₈₆ in the isomerization process, in both ground and excited states of the chromophore, and probably in fine tuning of the pK_a of the retinal in bR.