Literature DB >> 30721054

Assessment of MC-PDFT Excitation Energies for a Set of QM/MM Models of Rhodopsins.

María Del Carmen Marín1,2, Luca De Vico1, Sijia S Dong3, Laura Gagliardi3, Donald G Truhlar3, Massimo Olivucci1,2,4.   

Abstract

A methodology for the automatic production of quantum mechanical/molecular mechanical (QM/MM) models of retinal-binding rhodopsin proteins and subsequent prediction of their spectroscopic properties has been proposed recently by some of the authors. The technology employed for the evaluation of the excitation energies is called Automatic Rhodopsin Modeling (ARM), and it involves the use of the complete active space self-consistent field (CASSCF) method followed by a multiconfiguration second-order perturbation theory (in particular, CASPT2) calculation of external correlation energies. Although it was shown that ARM is capable of successfully reproducing and predicting spectroscopic property trends in chromophore-embedding protein sets, practical applications of such technology are limited by the high computational costs of the multiconfiguration perturbation theory calculations. In the present work we benchmark the more affordable multiconfiguration pair-density functional theory (MC-PDFT) method whose accuracy has been recently validated for retinal chromophores in the gas phase, indicating that MC-PDFT could potentially be used to analyze large (e.g., few hundreds) sets of rhodopsin proteins. Here, we test this theory for a set of rhodopsin QM/MM models whose experimental absorption maxima (λ a max) have been measured. The results indicate that MC-PDFT may be employed to calculate λ a max values for this important class of photoresponsive proteins.

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Year:  2019        PMID: 30721054      PMCID: PMC7096677          DOI: 10.1021/acs.jctc.8b01069

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  44 in total

1.  Density functional approximations for charge transfer excitations with intermediate spatial overlap.

Authors:  Ruifang Li; Jingjing Zheng; Donald G Truhlar
Journal:  Phys Chem Chem Phys       Date:  2010-08-24       Impact factor: 3.676

2.  Crystal structure of the 13-cis isomer of bacteriorhodopsin in the dark-adapted state.

Authors:  Taichi Nishikawa; Midori Murakami; Tsutomu Kouyama
Journal:  J Mol Biol       Date:  2005-09-16       Impact factor: 5.469

3.  Communication: extended multi-state complete active space second-order perturbation theory: energy and nuclear gradients.

Authors:  Toru Shiozaki; Werner Gyorffy; Paolo Celani; Hans-Joachim Werner
Journal:  J Chem Phys       Date:  2011-08-28       Impact factor: 3.488

Review 4.  Biophysics of Channelrhodopsin.

Authors:  Franziska Schneider; Christiane Grimm; Peter Hegemann
Journal:  Annu Rev Biophys       Date:  2015       Impact factor: 12.981

5.  Photochemical properties of mammalian melanopsin.

Authors:  Take Matsuyama; Takahiro Yamashita; Yasushi Imamoto; Yoshinori Shichida
Journal:  Biochemistry       Date:  2012-06-25       Impact factor: 3.162

Review 6.  Microbial Rhodopsins: Diversity, Mechanisms, and Optogenetic Applications.

Authors:  Elena G Govorunova; Oleg A Sineshchekov; Hai Li; John L Spudich
Journal:  Annu Rev Biochem       Date:  2017-03-09       Impact factor: 23.643

7.  An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems.

Authors:  Yoelvis Orozco-Gonzalez; Madushanka Manathunga; María Del Carmen Marín; Damianos Agathangelou; Kwang-Hwan Jung; Federico Melaccio; Nicolas Ferré; Stefan Haacke; Kaline Coutinho; Sylvio Canuto; Massimo Olivucci
Journal:  J Chem Theory Comput       Date:  2017-11-21       Impact factor: 6.006

8.  Optogenetics.

Authors:  Karl Deisseroth
Journal:  Nat Methods       Date:  2010-12-20       Impact factor: 28.547

9.  The IPEA dilemma in CASPT2.

Authors:  J Patrick Zobel; Juan J Nogueira; Leticia González
Journal:  Chem Sci       Date:  2016-09-26       Impact factor: 9.825

10.  Comparison of the isomerization mechanisms of human melanopsin and invertebrate and vertebrate rhodopsins.

Authors:  Silvia Rinaldi; Federico Melaccio; Samer Gozem; Francesca Fanelli; Massimo Olivucci
Journal:  Proc Natl Acad Sci U S A       Date:  2014-01-21       Impact factor: 11.205

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  3 in total

Review 1.  Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering.

Authors:  Willem J de Grip; Srividya Ganapathy
Journal:  Front Chem       Date:  2022-06-22       Impact factor: 5.545

Review 2.  Electronic structure of strongly correlated systems: recent developments in multiconfiguration pair-density functional theory and multiconfiguration nonclassical-energy functional theory.

Authors:  Chen Zhou; Matthew R Hermes; Dihua Wu; Jie J Bao; Riddhish Pandharkar; Daniel S King; Dayou Zhang; Thais R Scott; Aleksandr O Lykhin; Laura Gagliardi; Donald G Truhlar
Journal:  Chem Sci       Date:  2022-06-07       Impact factor: 9.969

Review 3.  Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol.

Authors:  Laura Pedraza-González; Luca De Vico; Massimo Olivucci; Leonardo Barneschi; Daniele Padula
Journal:  Top Curr Chem (Cham)       Date:  2022-03-15
  3 in total

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