{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1363670319450174464.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1021/jp709730b"}},{"identifier":{"@type":"URI","@value":"https://pubs.acs.org/doi/pdf/10.1021/jp709730b"}},{"identifier":{"@type":"PMID","@value":"18473437"}}],"dc:title":[{"@value":"Spectral Tuning in Visual Pigments: An ONIOM(QM:MM) Study on Bovine Rhodopsin and its Mutants"}],"description":[{"notation":[{"@value":"We have investigated geometries and excitation energies of bovine rhodopsin and some of its mutants by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in ONIOM scheme, employing B3LYP and BLYP density functionals as well as DFTB method for the QM part and AMBER force field for the MM part. QM/MM geometries of the protonated Schiff-base 11- cis-retinal with B3LYP and DFTB are very similar to each other. TD-B3LYP/MM excitation energy calculations reproduce the experimental absorption maximum of 500 nm in the presence of native rhodopsin environment and predict spectral shifts due to mutations within 10 nm, whereas TD-BLYP/MM excitation energies have red-shift error of at least 50 nm. In the wild-type rhodopsin, Glu113 shifts the first excitation energy to blue and accounts for most of the shift found. Other amino acids individually contribute to the first excitation energy but their net effect is small. The electronic polarization effect is essential for reproducing experimental bond length alternation along the polyene chain in protonated Schiff-base retinal, which correlates with the computed first excitation energy. It also corrects the excitation energies and spectral shifts in mutants, more effectively for deprotonated Schiff-base retinal than for the protonated form. The protonation state and conformation of mutated residues affect electronic spectrum significantly. The present QM/MM calculations estimate not only the experimental excitation energies but also the source of spectral shifts in mutants."}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1383670319450174464","@type":"Researcher","foaf:name":[{"@value":"Ahmet Altun"}],"jpcoar:affiliationName":[{"@value":"Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA, Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, Georgia 30322, USA, and Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo,Kyoto 606-8103, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670319450174466","@type":"Researcher","foaf:name":[{"@value":"Shozo Yokoyama"}],"jpcoar:affiliationName":[{"@value":"Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA, Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, Georgia 30322, USA, and Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo,Kyoto 606-8103, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670319450174465","@type":"Researcher","foaf:name":[{"@value":"Keiji Morokuma"}],"jpcoar:affiliationName":[{"@value":"Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA, Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, Georgia 30322, USA, and Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo,Kyoto 606-8103, Japan"}]}],"publication":{"publicationIdentifier":[{"@type":"PISSN","@value":"15206106"},{"@type":"EISSN","@value":"15205207"}],"prism:publicationName":[{"@value":"The Journal of Physical Chemistry B"}],"dc:publisher":[{"@value":"American Chemical Society (ACS)"}],"prism:publicationDate":"2008-05-13","prism:volume":"112","prism:number":"22","prism:startingPage":"6814","prism:endingPage":"6827"},"reviewed":"false","dcterms:accessRights":"http://purl.org/coar/access_right/c_abf2","url":[{"@id":"https://pubs.acs.org/doi/pdf/10.1021/jp709730b"}],"createdAt":"2008-05-13","modifiedAt":"2023-03-07","foaf:topic":[{"@id":"https://cir.nii.ac.jp/all?q=Models,%20Molecular","dc:title":"Models, Molecular"},{"@id":"https://cir.nii.ac.jp/all?q=Rhodopsin","dc:title":"Rhodopsin"},{"@id":"https://cir.nii.ac.jp/all?q=Light","dc:title":"Light"},{"@id":"https://cir.nii.ac.jp/all?q=Molecular%20Structure","dc:title":"Molecular Structure"},{"@id":"https://cir.nii.ac.jp/all?q=Crystallography,%20X-Ray","dc:title":"Crystallography, X-Ray"},{"@id":"https://cir.nii.ac.jp/all?q=Protein%20Structure,%20Tertiary","dc:title":"Protein Structure, Tertiary"},{"@id":"https://cir.nii.ac.jp/all?q=Models,%20Chemical","dc:title":"Models, Chemical"},{"@id":"https://cir.nii.ac.jp/all?q=Mutation","dc:title":"Mutation"},{"@id":"https://cir.nii.ac.jp/all?q=Animals","dc:title":"Animals"},{"@id":"https://cir.nii.ac.jp/all?q=Quantum%20Theory","dc:title":"Quantum Theory"},{"@id":"https://cir.nii.ac.jp/all?q=Cattle","dc:title":"Cattle"},{"@id":"https://cir.nii.ac.jp/all?q=Computer%20Simulation","dc:title":"Computer Simulation"}],"relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1360002216635589760","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"The ONIOM Method and Its Applications"}]},{"@id":"https://cir.nii.ac.jp/crid/1360285705052887552","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Color Tuning in Photofunctional Proteins"}]},{"@id":"https://cir.nii.ac.jp/crid/1360567183082189056","@type":"Article","resourceType":"学術雑誌論文(journal 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