Ab initio, tight-binding and QM/MM calculations of the rhodopsin chromophore in its binding pocket

We present results of ab initio and combined ab initio and force field calculations for the conformational changes of the rhodopsin chromophore in its binding pocket subject to various constraints like the inclusion of a water molecule near the counterion Glu113. Furthermore, the influence of other...

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Bibliographic Details
Published inPhase transitions Vol. 77; no. 1-2; pp. 31 - 45
Main Authors Sugihara, M., Buss, V., Entel, P., Hafner, J., Bondar, A.N., Elstner, M., Frauenheim, T.
Format Journal Article
LanguageEnglish
Published Taylor & Francis Group 01.01.2004
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ISSN0141-1594
1029-0338
DOI10.1080/1411590310001621564

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Summary:We present results of ab initio and combined ab initio and force field calculations for the conformational changes of the rhodopsin chromophore in its binding pocket subject to various constraints like the inclusion of a water molecule near the counterion Glu113. Furthermore, the influence of other charged groups on the stability of the protonated Schiff base is investigated as well as the role of the amino acid threonine (Thr94). The calculations yield a stable protonated Schiff base and a highly twisted conformation of the chromophore which is in agreement with the latest refined set of structure data.
ISSN:0141-1594
1029-0338
DOI:10.1080/1411590310001621564