title: Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology.
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.
authors: Department of Biotechnology, Chemistry e Pharmacy, Università di Siena , via A. Moro 2, I-53100 Siena, Italy.
authors: Federico
authors: F
authors: Melaccio
authors: Department of Biotechnology, Chemistry e Pharmacy, Università di Siena , via A. Moro 2, I-53100 Siena, Italy.|Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States.
authors: María
authors: M
authors: Del Carmen Marín
authors: Department of Biotechnology, Chemistry e Pharmacy, Università di Siena , via A. Moro 2, I-53100 Siena, Italy.
authors: Alessio
authors: A
authors: Valentini
authors: Department of Biotechnology, Chemistry e Pharmacy, Università di Siena , via A. Moro 2, I-53100 Siena, Italy.
authors: Fabio
authors: F
authors: Montisci
authors: Department of Biotechnology, Chemistry e Pharmacy, Università di Siena , via A. Moro 2, I-53100 Siena, Italy.
authors: Silvia
authors: S
authors: Rinaldi
authors: Department of Biotechnology, Chemistry e Pharmacy, Università di Siena , via A. Moro 2, I-53100 Siena, Italy.
authors: Marco
authors: M
authors: Cherubini
authors: Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States.
authors: Xuchun
authors: X
authors: Yang
authors: Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya, Japan.
authors: Yoshitaka
authors: Y
authors: Kato
authors: Aix-Marseille Université , CNRS, ICR, 13284 Marseille, France.
authors: Michael
authors: M
authors: Stenrup
authors: Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States.|Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 Université de Strasbourg-CNRS , F-67034 Strasbourg, France.|USIAS Institut d'Études Avancées, Université de Strasbourg , 5 allée du Général Rouvillois, F-67083 Strasbourg, France.
authors: Yoelvis
authors: Y
authors: Orozco-Gonzalez
authors: Aix-Marseille Université , CNRS, ICR, 13284 Marseille, France.
authors: Nicolas
authors: N
authors: Ferré
authors: Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States.
authors: Hoi Ling
authors: HL
authors: Luk
authors: Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya, Japan.
authors: Hideki
authors: H
authors: Kandori
authors: Department of Biotechnology, Chemistry e Pharmacy, Università di Siena , via A. Moro 2, I-53100 Siena, Italy.|Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States.|Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 Université de Strasbourg-CNRS , F-67034 Strasbourg, France.|USIAS Institut d'Études Avancées, Université de Strasbourg , 5 allée du Général Rouvillois, F-67083 Strasbourg, France.
authors: Massimo
authors: M
authors: Olivucci
mesh_terms: D000818:Animals; D001105:Archaea / Q000378:metabolism; D019843:Archaeal Proteins / Q000737:chemistry / Q000378:metabolism; D001331:Automation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D011789:Quantum Theory; D012172:Retinaldehyde / Q000737:chemistry; D012243:Rhodopsin / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D019843:Archaeal Proteins; D012243:Rhodopsin; D012172:Retinaldehyde