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...

Full description

Saved in:
Bibliographic Details
Published in:Journal of chemical theory and computation Vol. 12; no. 12; pp. 6020 - 6034
Main Authors: 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
Language:English
Published: United States 13.12.2016
Subjects:
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
Online Access:Get more information
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1549-9626
DOI:10.1021/acs.jctc.6b00367