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Field MJ. pDynamo3 Molecular Modeling and Simulation Program. J Chem Inf Model 2022; 62:5849-5854. [PMID: 36449463 DOI: 10.1021/acs.jcim.2c01239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
pDynamo3 is the first formal version of the Dynamo molecular modeling and simulation library that is written in Python 3. It follows from the previous pDynamo versions written in Python 2, the first of which was released in 2007. Both pDynamo and its predecessor, fDynamo, were designed with the aim of providing easy-to-use and flexible frameworks for performing molecular simulations at an atomistic level with a special emphasis on those employing hybrid quantum chemical and molecular mechanical potential methods. Although the use of pDynamo3 is quite similar to that of pDynamo2, it has added significant new capability and also undergone extensive restructuring that will make it much easier to extend with new functionality. The pDynamo3 code is issued under the GNU general public license at https://github.com/pdynamo/pDynamo3 with additional information on the pDynamo website https:www.pdynamo.org.
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Affiliation(s)
- Martin J Field
- Laboratoire de Chimie et Biologie des Métaux, UMR5249, Université Grenoble I, CEA, CNRS, 17 avenue des Martyrs, 38054 Cedex 9, Grenoble, France.,Theory Group, Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Cedex 9, Grenoble, France
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Barroso da Silva FL, Sterpone F, Derreumaux P. OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field. J Chem Theory Comput 2019; 15:3875-3888. [DOI: 10.1021/acs.jctc.9b00202] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fernando Luís Barroso da Silva
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do café, s/no, Ribeirão Preto, São Paulo BR-14040-903, Brazil
- Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot − Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Fabio Sterpone
- Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot − Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
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Corbella M, Toa ZSD, Scholes GD, Luque FJ, Curutchet C. Determination of the protonation preferences of bilin pigments in cryptophyte antenna complexes. Phys Chem Chem Phys 2018; 20:21404-21416. [PMID: 30105318 DOI: 10.1039/c8cp02541j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The light-harvesting mechanisms of cryptophyte antenna complexes have attracted considerable attention due to their ability to exhibit maximal photosynthetic activity under very low-light conditions and to display several colors, as well as the observation of vibronic coherent features in their two-dimensional electronic spectra. However, detailed investigations on the interplay between the protein environment and their light-harvesting properties are hampered by the uncertainty related to the protonation state of the underlying bilin pigments. Here we study the protonation preferences of four types of bilin pigments including 15,16-dihydrobiliverdin (DBV), phycoerythrobilin (PEB), phycocyanobilin (PCB) and mesobiliverdin (MBV), which are found in phycoerythrin PE545 and phycocyanin PC577, PC612, PC630 and PC645 complexes. We apply quantum chemical calculations coupled to continuum solvation calculations to predict the intrinsic acidity of bilins in aqueous solution, and then combine molecular dynamics simulations with empirical pKa estimates to investigate the impact of the local protein environment on the acidity of the pigments. We also report measurements of the absorption spectra of the five complexes in a wide range of pH in order to validate our simulations and investigate possible changes in the light harvesting properties of the complexes in the range of physiological pH found in the lumen (pH ∼ 5-7). The results suggest a pKa > 7 for DBV and MBV pigments in the α polypeptide chains of PE545 and PC630/PC645 complexes, which are not coordinated to a negatively charged amino acid. For the other PEB, DBV and PCB pigments, which interact with a Glu or Asp side chain, higher pKa values (pKa > 8) are estimated. Overall, the results support a preferential population of the fully protonated state for bilins in cryptophyte complexes under physiological conditions regardless of the specific type of pigment and local protein environment.
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Affiliation(s)
- Marina Corbella
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Química Teòrica i Computacional (IQTCUB), Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.
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Shaik MM, Bhattacharjee N, Feliks M, Ng KKS, Field MJ. Norovirus RNA-dependent RNA polymerase: A computational study of metal-binding preferences. Proteins 2017; 85:1435-1445. [PMID: 28383118 DOI: 10.1002/prot.25304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 03/31/2017] [Accepted: 04/04/2017] [Indexed: 12/21/2022]
Abstract
Norovirus (NV) RNA-dependent RNA polymerase (RdRP) is essential for replicating the genome of the virus, which makes this enzyme a key target for the development of antiviral agents against NV gastroenteritis. In this work, a complex of NV RdRP bound to manganese ions and an RNA primer-template duplex was investigated using X-ray crystallography and hybrid quantum chemical/molecular mechanical simulations. Experimentally, the complex crystallized in a tetragonal crystal form. The nature of the primer/template duplex binding in the resulting structure indicates that the complex is a closed back-tracked state of the enzyme, in which the 3'-end of the primer occupies the position expected for the post-incorporated nucleotide before translocation. Computationally, it is found that the complex can accept a range of divalent metal cations without marked distortions in the active site structure. The highest binding energy is for copper, followed closely by manganese and iron, and then by zinc, nickel, and cobalt. Proteins 2017; 85:1435-1445. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Md Munan Shaik
- Division of Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, 02115.,Department of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, Massachusetts, 02115
| | - Nicholus Bhattacharjee
- Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, Grenoble Cedex 9, 38044, France
| | - Mikolaj Feliks
- Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, Grenoble Cedex 9, 38044, France
| | - Kenneth K-S Ng
- Department of Biological Sciences and Alberta Glycomics Centre, University of Calgary, Calgary, Alberta, Canada
| | - Martin J Field
- Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, Grenoble Cedex 9, 38044, France
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Bhattacharjee N, Feliks M, Shaik MM, Field MJ. Catalytic Mechanism of Peptidoglycan Deacetylase: A Computational Study. J Phys Chem B 2016; 121:89-99. [DOI: 10.1021/acs.jpcb.6b10625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicholus Bhattacharjee
- Dynamo
Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
| | - Mikolaj Feliks
- Dynamo
Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
| | - Md Munan Shaik
- Division
of Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, Massachusetts 02115, United States
| | - Martin J. Field
- Dynamo
Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
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Feliks M, Lafaye C, Shu X, Royant A, Field M. Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations. Biochemistry 2016; 55:4263-74. [DOI: 10.1021/acs.biochem.6b00295] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mikolaj Feliks
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Céline Lafaye
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Xiaokun Shu
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
- Cardiovascular
Research Institute, University of California, San Francisco, California 94158, United States
| | - Antoine Royant
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Martin Field
- Université Grenoble Alpes, Institut de Biologie Structurale
(IBS), F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
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