Literature DB >> 33369749

Frontiers in Multiscale Modeling of Photoreceptor Proteins.

Maria-Andrea Mroginski1, Suliman Adam2, Gil S Amoyal2, Avishai Barnoy2, Ana-Nicoleta Bondar3, Veniamin A Borin2, Jonathan R Church2, Tatiana Domratcheva4,5, Bernd Ensing6, Francesca Fanelli7, Nicolas Ferré8, Ofer Filiba2, Laura Pedraza-González9, Ronald González1, Cristina E González-Espinoza10, Rajiv K Kar2, Lukas Kemmler3, Seung Soo Kim11, Jacob Kongsted12, Anna I Krylov13, Yigal Lahav2,14, Michalis Lazaratos3, Qays NasserEddin2, Isabelle Navizet15, Alexander Nemukhin4,16, Massimo Olivucci9,17, Jógvan Magnus Haugaard Olsen18,19, Alberto Pérez de Alba Ortíz6, Elisa Pieri8, Aditya G Rao2, Young Min Rhee11, Niccolò Ricardi10, Saumik Sen2, Ilia A Solov'yov20, Luca De Vico9, Tomasz A Wesolowski10, Christian Wiebeler2, Xuchun Yang17, Igor Schapiro2.   

Abstract

This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.
© 2021 American Society for Photobiology.

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Year:  2021        PMID: 33369749      PMCID: PMC9185909          DOI: 10.1111/php.13372

Source DB:  PubMed          Journal:  Photochem Photobiol        ISSN: 0031-8655            Impact factor:   3.521


  154 in total

1.  Coupling of retinal, protein, and water dynamics in squid rhodopsin.

Authors:  Eduardo Jardón-Valadez; Ana-Nicoleta Bondar; Douglas J Tobias
Journal:  Biophys J       Date:  2010-10-06       Impact factor: 4.033

2.  GROMACS: fast, flexible, and free.

Authors:  David Van Der Spoel; Erik Lindahl; Berk Hess; Gerrit Groenhof; Alan E Mark; Herman J C Berendsen
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

3.  The Amber biomolecular simulation programs.

Authors:  David A Case; Thomas E Cheatham; Tom Darden; Holger Gohlke; Ray Luo; Kenneth M Merz; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J Woods
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

4.  Relative ground and excited-state pKa values of phytochromobilin in the photoactivation of phytochrome: a computational study.

Authors:  O Anders Borg; Bo Durbeej
Journal:  J Phys Chem B       Date:  2007-09-11       Impact factor: 2.991

5.  The role of solvation models on the computed absorption and emission spectra: the case of fireflies oxyluciferin.

Authors:  Cristina García-Iriepa; Madjid Zemmouche; Miguel Ponce-Vargas; Isabelle Navizet
Journal:  Phys Chem Chem Phys       Date:  2019-02-20       Impact factor: 3.676

6.  Photo Control of Protein Function Using Photoactive Yellow Protein.

Authors:  Jakeb M Reis; G Andrew Woolley
Journal:  Methods Mol Biol       Date:  2016

7.  Early Photocycle of Slr1694 Blue-Light Using Flavin Photoreceptor Unraveled through Adiabatic Excited-State Quantum Mechanical/Molecular Mechanical Dynamics.

Authors:  Joshua J Goings; Sharon Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2019-12-10       Impact factor: 15.419

8.  Theoretical Studies on the Color-Tuning Mechanism in Retinal Proteins.

Authors:  Kazuhiro Fujimoto; Shigehiko Hayashi; Jun-Ya Hasegawa; Hiroshi Nakatsuji
Journal:  J Chem Theory Comput       Date:  2007-03       Impact factor: 6.006

9.  Bridge: A Graph-Based Algorithm to Analyze Dynamic H-Bond Networks in Membrane Proteins.

Authors:  Malte Siemers; Michalis Lazaratos; Konstantina Karathanou; Federico Guerra; Leonid S Brown; Ana-Nicoleta Bondar
Journal:  J Chem Theory Comput       Date:  2019-11-11       Impact factor: 6.006

10.  Introducing VIKING: A Novel Online Platform for Multiscale Modeling.

Authors:  Vasili Korol; Peter Husen; Emil Sjulstok; Claus Nielsen; Ida Friis; Anders Frederiksen; Adrian B Salo; Ilia A Solov'yov
Journal:  ACS Omega       Date:  2019-12-17
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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

2.  Pro219 is an electrostatic color determinant in the light-driven sodium pump KR2.

Authors:  Yuta Nakajima; Laura Pedraza-González; Leonardo Barneschi; Keiichi Inoue; Massimo Olivucci; Hideki Kandori
Journal:  Commun Biol       Date:  2021-10-13

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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