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

Minoru Sugihara; Volker Buss; Peter Entel; Juergen Hafner; A A Bondar; Marcus Elstner; T Frauenheim

doi:10.1080/1411590310001621564

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

Minoru Sugihara, Volker Buss, Peter Entel, Juergen Hafner, A A Bondar, Marcus Elstner, T Frauenheim

Veröffentlichungen: Beitrag in Fachzeitschrift › Meeting Abstract/Conference Paper

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 Glul 13. 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.

Originalsprache	Englisch
Seiten (von - bis)	31-45
Seitenumfang	15
Fachzeitschrift	Phase Transitions: a multinational journal
Jahrgang	77
Ausgabenummer	1-2
DOIs	https://doi.org/10.1080/1411590310001621564
Publikationsstatus	Veröffentlicht - 2004

ÖFOS 2012

1030 Physik, Astronomie

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10.1080/1411590310001621564

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

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 Glul 13. 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 = "Minoru Sugihara and Volker Buss and Peter Entel and Juergen Hafner and Bondar, {A A} and Marcus Elstner and T Frauenheim",

note = "DOI: 10.1080/1411590310001621564 Coden: PHTRD Affiliations: Institute of Physics, University of Duisburg-Essen, 47048 Duisburg, Germany; Institute of Chemistry, University of Duisburg-Essen, 47048 Duisburg, Germany; Ctr. for Compl. Materials Science, University of Vienna, 1098 Vienna, Austria; IWR, Computational Molecular Physics, University of Heidelberg, 69120, Heidelberg, Germany; Institute of Physics, University of Paderborn, 33098 Paderborn, Germany Adressen: Sugihara, M.; Institute of Physics; University of Duisburg-Essen 47048 Duisburg, Germany; email: [email protected] Import aus Scopus: 2-s2.0-4644221934 22.10.2007: Datenanforderung 1935 (Import Sachbearbeiter) 22.10.2007: Datenanforderung 1936 (Import Sachbearbeiter)",

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doi = "10.1080/1411590310001621564",

language = "English",

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T1 - Ab initio, tight-binding and QM/MM calculations of the rhodopsin chromophore in its binding pocket

AU - Sugihara, Minoru

AU - Buss, Volker

AU - Entel, Peter

AU - Hafner, Juergen

AU - Bondar, A A

AU - Elstner, Marcus

AU - Frauenheim, T

N1 - DOI: 10.1080/1411590310001621564 Coden: PHTRD Affiliations: Institute of Physics, University of Duisburg-Essen, 47048 Duisburg, Germany; Institute of Chemistry, University of Duisburg-Essen, 47048 Duisburg, Germany; Ctr. for Compl. Materials Science, University of Vienna, 1098 Vienna, Austria; IWR, Computational Molecular Physics, University of Heidelberg, 69120, Heidelberg, Germany; Institute of Physics, University of Paderborn, 33098 Paderborn, Germany Adressen: Sugihara, M.; Institute of Physics; University of Duisburg-Essen 47048 Duisburg, Germany; email: [email protected] Import aus Scopus: 2-s2.0-4644221934 22.10.2007: Datenanforderung 1935 (Import Sachbearbeiter) 22.10.2007: Datenanforderung 1936 (Import Sachbearbeiter)

PY - 2004

Y1 - 2004

N2 - 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 Glul 13. 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.

AB - 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 Glul 13. 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.

U2 - 10.1080/1411590310001621564

DO - 10.1080/1411590310001621564

M3 - Meeting abstract/Conference paper

SN - 0141-1594

VL - 77

SP - 31

EP - 45

JO - Phase Transitions: a multinational journal

JF - Phase Transitions: a multinational journal

IS - 1-2

ER -

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

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ÖFOS 2012

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