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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| Published in | Phase transitions Vol. 77; no. 1-2; pp. 31 - 45 |
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| Main Authors | , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Taylor & Francis Group
01.01.2004
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0141-1594 1029-0338 |
| DOI | 10.1080/1411590310001621564 |
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| Abstract | 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. |
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| AbstractList | 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. |
| Author | Entel, P. Buss, V. Sugihara, M. Hafner, J. Bondar, A.N. Frauenheim, T. Elstner, M. |
| Author_xml | – sequence: 1 givenname: M. surname: Sugihara fullname: Sugihara, M. organization: Institute of Physics , University of Duisburg-Essen – sequence: 2 givenname: V. surname: Buss fullname: Buss, V. organization: Institute of Chemistry , University of Duisburg-Essen – sequence: 3 givenname: P. surname: Entel fullname: Entel, P. organization: Institute of Physics , University of Duisburg-Essen – sequence: 4 givenname: J. surname: Hafner fullname: Hafner, J. organization: Center for Computational Materials Science , University of Vienna – sequence: 5 givenname: A.N. surname: Bondar fullname: Bondar, A.N. organization: IWR , Computational Molecular Physics, University of Heidelberg – sequence: 6 givenname: M. surname: Elstner fullname: Elstner, M. organization: Institute of Physics , University of Paderborn – sequence: 7 givenname: T. surname: Frauenheim fullname: Frauenheim, T. organization: Institute of Physics , University of Paderborn |
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| SubjectTerms | Rhodopsin; Ab initio molecular dynamics and force field simulations |
| Title | Ab initio, tight-binding and QM/MM calculations of the rhodopsin chromophore in its binding pocket |
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