Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology

We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their mutants. In the present implementation the information required for the construction of each model is essentially a crystallographic structure or...

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Veröffentlicht in:Journal of chemical theory and computation Jg. 12; H. 12; S. 6020 - 6034
Hauptverfasser: Melaccio, Federico, Del Carmen Marín, María, Valentini, Alessio, Montisci, Fabio, Rinaldi, Silvia, Cherubini, Marco, Yang, Xuchun, Kato, Yoshitaka, Stenrup, Michael, Orozco-Gonzalez, Yoelvis, Ferré, Nicolas, Luk, Hoi Ling, Kandori, Hideki, Olivucci, Massimo
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States 13.12.2016
Schlagworte:
Animals
Archaea - metabolism
Archaeal Proteins - chemistry
Archaeal Proteins - metabolism
Automation
Hydrogen Bonding
Models, Molecular
Protein Structure, Tertiary
Quantum Theory
Retinaldehyde - chemistry
Rhodopsin - chemistry
Rhodopsin - metabolism
Thermodynamics
ISSN:1549-9626
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Abstract We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their mutants. In the present implementation the information required for the construction of each model is essentially a crystallographic structure or a comparative model complemented with information on the protonation state of ionizable side chains and distributions of external counterions. Starting with such information, a model formed by a fixed environment system, a flexible cavity system, and a chromophore system is automatically generated. The results of the predicted vertical excitation energy for 27 different rhodopsins including vertebrate, invertebrate, and microbial pigments indicate that such basic models could be employed for predicting trends in spectral changes and/or correlate the spectral changes with structural variations in large sets of proteins.
AbstractList We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their mutants. In the present implementation the information required for the construction of each model is essentially a crystallographic structure or a comparative model complemented with information on the protonation state of ionizable side chains and distributions of external counterions. Starting with such information, a model formed by a fixed environment system, a flexible cavity system, and a chromophore system is automatically generated. The results of the predicted vertical excitation energy for 27 different rhodopsins including vertebrate, invertebrate, and microbial pigments indicate that such basic models could be employed for predicting trends in spectral changes and/or correlate the spectral changes with structural variations in large sets of proteins.
Author Rinaldi, Silvia
Del Carmen Marín, María
Valentini, Alessio
Montisci, Fabio
Olivucci, Massimo
Melaccio, Federico
Kandori, Hideki
Cherubini, Marco
Stenrup, Michael
Yang, Xuchun
Orozco-Gonzalez, Yoelvis
Luk, Hoi Ling
Ferré, Nicolas
Kato, Yoshitaka
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  givenname: Federico
  surname: Melaccio
  fullname: Melaccio, Federico
  organization: Department of Biotechnology, Chemistry e Pharmacy, Università di Siena , via A. Moro 2, I-53100 Siena, Italy
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  givenname: María
  surname: Del Carmen Marín
  fullname: Del Carmen Marín, María
  organization: Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
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  givenname: Alessio
  surname: Valentini
  fullname: Valentini, Alessio
  organization: Department of Biotechnology, Chemistry e Pharmacy, Università di Siena , via A. Moro 2, I-53100 Siena, Italy
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  givenname: Fabio
  surname: Montisci
  fullname: Montisci, Fabio
  organization: Department of Biotechnology, Chemistry e Pharmacy, Università di Siena , via A. Moro 2, I-53100 Siena, Italy
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  givenname: Silvia
  surname: Rinaldi
  fullname: Rinaldi, Silvia
  organization: Department of Biotechnology, Chemistry e Pharmacy, Università di Siena , via A. Moro 2, I-53100 Siena, Italy
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  givenname: Marco
  surname: Cherubini
  fullname: Cherubini, Marco
  organization: Department of Biotechnology, Chemistry e Pharmacy, Università di Siena , via A. Moro 2, I-53100 Siena, Italy
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  givenname: Xuchun
  surname: Yang
  fullname: Yang, Xuchun
  organization: Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
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  givenname: Yoshitaka
  surname: Kato
  fullname: Kato, Yoshitaka
  organization: Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya, Japan
– sequence: 9
  givenname: Michael
  surname: Stenrup
  fullname: Stenrup, Michael
  organization: Aix-Marseille Université , CNRS, ICR, 13284 Marseille, France
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  givenname: Yoelvis
  surname: Orozco-Gonzalez
  fullname: Orozco-Gonzalez, Yoelvis
  organization: USIAS Institut d'Études Avancées, Université de Strasbourg , 5 allée du Général Rouvillois, F-67083 Strasbourg, France
– sequence: 11
  givenname: Nicolas
  surname: Ferré
  fullname: Ferré, Nicolas
  organization: Aix-Marseille Université , CNRS, ICR, 13284 Marseille, France
– sequence: 12
  givenname: Hoi Ling
  surname: Luk
  fullname: Luk, Hoi Ling
  organization: Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
– sequence: 13
  givenname: Hideki
  surname: Kandori
  fullname: Kandori, Hideki
  organization: Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya, Japan
– sequence: 14
  givenname: Massimo
  surname: Olivucci
  fullname: Olivucci, Massimo
  organization: USIAS Institut d'Études Avancées, Université de Strasbourg , 5 allée du Général Rouvillois, F-67083 Strasbourg, France
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Snippet We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their...
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SubjectTerms Animals
Archaea - metabolism
Archaeal Proteins - chemistry
Archaeal Proteins - metabolism
Automation
Hydrogen Bonding
Models, Molecular
Protein Structure, Tertiary
Quantum Theory
Retinaldehyde - chemistry
Rhodopsin - chemistry
Rhodopsin - metabolism
Thermodynamics
Title Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology
URI https://www.ncbi.nlm.nih.gov/pubmed/27779842
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