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. 2010 Jan 21;1(3):668-672.
doi: 10.1021/jz100026k.

Drawing the Retinal Out of Its Comfort Zone: An ONIOM(QM/MM) Study of Mutant Squid Rhodopsin

Sivakumar Sekharan  1 , Keiji Morokuma
Affiliations

Drawing the Retinal Out of Its Comfort Zone: An ONIOM(QM/MM) Study of Mutant Squid Rhodopsin

Sivakumar Sekharan et al. J Phys Chem Lett. .

Abstract

Engineering squid rhodopsin with modified retinal analogues is essential for understanding the conserved steric and electrostatic interaction networks that govern the architecture of the Schiff base binding site. Depriving the retinal of its steric and electrostatic contacts affects the positioning of the Schiff-base relative to the key residues Asn87, Tyr111, and Glu180. Displacement of the W1 and W2 positions and the impact on the structural rearrangements near the Schiff base binding region reiterates the need for the presence of internal water molecules and the accessibility of binding sites to them. Also, the dominant role of the Glu180 counterion in inducing the S(1)/S(2) state reversal for SBR is shown for the first time in squid rhodopsin.

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Figures

Figure 1
Figure 1
Optimized QM/MM geometries of (A) wildtype (WT) in red, (B) demethyl (DM) in black, (C) deprotonated (SBRcip) in the presence of protonated counterion Glu180 in green, and (D) deprotonated (SBRcidp) in the presence of deprotonated counterion Glu180 in cyan. Also shown are the distances (black dashed lines) between SBN+ or the SBN atom to the OH atom of Tyr111 (ochre), the OD1 atom of Asn87 (magenta), the OE2 atom of Glu180 (yellow), and the C5 atom of the retinal. Also shown are the two internal water molecules W1 and W2 (blue circles) near the SB.
Figure 2
Figure 2
Comparison of the bond length alternation (bottom), bond angles (middle), and dihedral angles (top) along the conjugated carbon chain of the optimized QM/MM wildtype PSBR (red), demethyl PSBR (black), deprotonated SBRcip (green), and SBRcidp (blue) geometries. The dihedral angle deviations are from either the cis (0°) or the trans (180°) configuration.
See this image and copyright information in PMC

References

    1. Murakami M, Kouyama T. Crystal Structure of Squid Rhodopsin. Nature. 2008;453:363–367. - PubMed
    1. Shimamura T, Hiraki N, Takahashi T, Hori H, Ago K, Masuda K, Takio M, Ishiguro M, Miyano M. Crystal Structure of Squid Rhodopsin with Intracellularly Extended Cytoplasmic Region. J Biol Chem. 2008;283:17753–17756. - PMC - PubMed
    1. Sekharan S, Altun A, Morokuma K. Photochemistry of Visual Pigment in a Gq Protein-Coupled Receptor (GPCR)—Insights from Structural and Spectral Tuning Studies on Squid Rhodopsin. Chem—Eur J. 2010 doi: 10.1002/chem.200903194. - DOI - PMC - PubMed
    1. Birge RR. Photophysics and Molecular Electronic Applications of the Rhodopsins. Annu Rev Phys Chem. 1990;41:683–733. - PubMed
    1. Vreven T, Byun KS, Komáromi I, Dapprich S, Montgomery JA, Jr, Morokuma K, Frisch MJ. Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM. J Chem Theory Comput. 2006;2:815–826. - PubMed