title: Drawing the Retinal Out of Its Comfort Zone: An ONIOM(QM/MM) Study of Mutant Squid Rhodopsin.
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.
authors.affiliation: Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322.
authors.forename: Sivakumar
authors.initials: S
authors.lastname: Sekharan
authors.forename: Keiji
authors.initials: K
authors.lastname: Morokuma
references.citation: Chemphyschem. 2005 Sep 5;6(9):1836-47
references.pmid: 16110519
references.citation: Proc Natl Acad Sci U S A. 1985 Jun;82(12):4117-21
references.pmid: 2987964
references.citation: Nature. 2008 May 15;453(7193):363-7
references.pmid: 18480818
references.citation: J Phys Chem B. 2008 Dec 25;112(51):16883-90
references.pmid: 19367945
references.citation: Chemistry. 2010 Feb 8;16(6):1744-9
references.pmid: 20066712
references.citation: Annu Rev Phys Chem. 1990;41:683-733
references.pmid: 2257039
references.citation: J Chem Theory Comput. 2006 May;2(3):815-26
references.pmid: 26626688
references.citation: Biochim Biophys Acta. 1978 Dec 7;504(3):413-30
references.pmid: 718881
references.citation: Biochemistry. 2006 Jan 24;45(3):801-10
references.pmid: 16411756
references.citation: J Am Chem Soc. 2007 Oct 31;129(43):13035-42
references.pmid: 17924622
references.citation: J Am Chem Soc. 2007 Feb 7;129(5):1052-4
references.pmid: 17263385
references.citation: Phys Chem Chem Phys. 2007 Jun 14;9(22):2862-7
references.pmid: 17538731
references.citation: J Biol Chem. 2008 Jun 27;283(26):17753-6
references.pmid: 18463093
references.citation: J Mol Model. 2008 Aug;14(8):717-26
references.pmid: 18351404
references.citation: Nature. 1967 May 6;214(5088):572-3
references.pmid: 6036170
references.citation: J Gen Physiol. 1958 Jan 20;41(3):501-28
references.pmid: 13491819
references.citation: Acc Chem Res. 2006 Mar;39(3):184-93
references.pmid: 16548507