Galvani Offset Potential and Constant-pH Simulations of Membrane Proteins.

Hydrogen-Ion Concentration Membrane Proteins Molecular Dynamics Simulation Water / chemistry

Journal

The journal of physical chemistry. B
ISSN: 1520-5207
Titre abrégé: J Phys Chem B
Pays: United States
ID NLM: 101157530

Informations de publication

Date de publication:
15 09 2022
Historique:
pubmed: 2 9 2022
medline: 17 9 2022
entrez: 1 9 2022
Statut: ppublish

Résumé

A central problem in computational biophysics is the treatment of titratable residues in molecular dynamics simulations of large biological macromolecular systems. Conventional simulation methods ascribe a fixed ionization state to titratable residues in accordance with their p

Identifiants

DOI: 10.1021/acs.jpcb.2c04593 PMID: 36049129 PMC: PMC9483922
pubmed: 36049129
doi: 10.1021/acs.jpcb.2c04593
pmc: PMC9483922
doi:

Substances chimiques

Membrane Proteins 0
Water 059QF0KO0R

Types de publication

Journal Article Research Support, Non-U.S. Gov't Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

6868-6877

Subventions

Organisme : NIGMS NIH HHS
ID : R01 GM072558
Pays : United States

Références

Methods Mol Biol. 2021;2315:185-195
pubmed: 34302677
J Phys Chem A. 2017 Feb 23;121(7):1525-1530
pubmed: 28152306
J Chem Phys. 2008 Dec 21;129(23):234706
pubmed: 19102551
Elife. 2020 Sep 11;9:
pubmed: 32915133
Trends Neurosci. 2006 Oct;29(10):578-86
pubmed: 16891000
J Chem Theory Comput. 2011 Aug 9;7(8):2617-29
pubmed: 26606635
J Chem Theory Comput. 2014 Jul 8;10(7):2690-709
pubmed: 26586504
Methods Mol Biol. 2021;2302:275-287
pubmed: 33877633
J Comput Chem. 2009 Jul 30;30(10):1545-614
pubmed: 19444816
J Chem Phys. 2007 Apr 28;126(16):164112
pubmed: 17477594
Biophys J. 2009 Jul 8;97(1):50-8
pubmed: 19580743
PLoS One. 2018 Dec 10;13(12):e0209147
pubmed: 30532181
J Chem Phys. 2016 Oct 7;145(13):134109
pubmed: 27782441
Biophys J. 2002 Feb;82(2):772-80
pubmed: 11806919
Biophys J. 2013 Aug 20;105(4):L15-7
pubmed: 23972860
Pharmacol Res. 2020 Apr;154:104166
pubmed: 30731197
J Chem Theory Comput. 2016 Apr 12;12(4):1449-1458
pubmed: 26918826
Front Mol Biosci. 2020 Apr 28;7:58
pubmed: 32411719
J Chem Phys. 2012 Nov 14;137(18):184105
pubmed: 23163362
J Chem Theory Comput. 2016 Nov 8;12(11):5411-5421
pubmed: 27709966
Nature. 2018 Mar 15;555(7696):397-401
pubmed: 29513651
J Chem Theory Comput. 2017 Dec 12;13(12):5933-5944
pubmed: 29111720
Chem Rev. 2014 Jan 8;114(1):779-814
pubmed: 23981057
Pharmacol Rev. 2015;67(1):1-35
pubmed: 25287517
J Chem Phys. 2020 Jul 28;153(4):044130
pubmed: 32752662
J Phys Chem B. 1998 Apr 30;102(18):3586-616
pubmed: 24889800
J Chem Phys. 1989 May 1;90(9):5211-3
pubmed: 11542468
Proteins. 1997 Apr;27(4):523-44
pubmed: 9141133
Biophys J. 2005 Jun;88(6):3745-61
pubmed: 15764651
J Chem Theory Comput. 2011 Jun 14;7(6):1962-1978
pubmed: 21687785
Neuron. 2002 Apr 25;34(3):463-77
pubmed: 11988176
J Phys Chem B. 2010 Jun 17;114(23):7830-43
pubmed: 20496934
Methods Enzymol. 2009;466:455-75
pubmed: 21609872
Cell. 2009 Nov 25;139(5):1012-21
pubmed: 19945383
J Chem Theory Comput. 2017 Dec 12;13(12):6405-6414
pubmed: 29117682
J Chem Theory Comput. 2012 Sep 11;8(9):3257-3273
pubmed: 23341755
J Chem Theory Comput. 2014 Mar 11;10(3):1341-1352
pubmed: 24803862
Biophys J. 2005 Jul;89(1):141-57
pubmed: 15863480
J Chem Theory Comput. 2015 Aug 11;11(8):3919-31
pubmed: 26300709
Nat Methods. 2017 Jan;14(1):71-73
pubmed: 27819658
Nat Rev Neurosci. 2013 Jul;14(7):461-71
pubmed: 23783197
Proteins. 2004 Sep 1;56(4):738-52
pubmed: 15281127
Biochemistry. 2006 Aug 8;45(31):9363-73
pubmed: 16878971

Auteurs

Olivier Bignucolo (O)

Department of Biomedical Sciences, University of Lausanne, 1015 Lausanne, Switzerland.
SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
ORCID: 0000-0003-4735-049X

Christophe Chipot (C)

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States.
Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche n◦7019, Université de Lorraine, B.P. 70239, 54506 Cedex Vandœuvre-lès-Nancy, France.
Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, United States.
ORCID: 0000-0002-9122-1698

Stephan Kellenberger (S)

Department of Biomedical Sciences, University of Lausanne, 1015 Lausanne, Switzerland.
ORCID: 0000-0003-1755-6198

Benoît Roux (B)

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States.
Department of Chemistry, The University of Chicago, 5735 S. Ellis Ave., Chicago, Illinois 60637, United States.
ORCID: 0000-0002-5254-2712

Articles similaires

Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells.

Daipayan Sarkar, Christopher Maffeo, Markus Sutter et al.
1.00
Photosynthesis Ribulose-Bisphosphate Carboxylase Carbon Dioxide Molecular Dynamics Simulation Cyanobacteria

Initial pH determines the morphological characteristics and secondary metabolite production in Aspergillus terreus and Streptomyces rimosus cocultures.

Tomasz Boruta, Martyna Foryś, Weronika Pawlikowska et al.
1.00
Aspergillus Hydrogen-Ion Concentration Coculture Techniques Secondary Metabolism Streptomyces rimosus

Effects of water-insoluble wheat bran-fraction powder on disease activity and caecal microbiota in dextran sodium sulphate-induced inflammatory bowel disease mouse model.

Kazuya Koga, Mizuki Sato, Nanase Okamoto et al.
1.00
Animals Dietary Fiber Dextran Sulfate Mice Disease Models, Animal

Study on the mechanical properties of granite responses of cyclic heating and water cooling considering microcosmic and energy.

Xiaokang Liang, Hanxiang Liu, Yong Yuan et al.
1.00
Silicon Dioxide Water Hot Temperature Compressive Strength X-Ray Diffraction

Classifications MeSH

questionsmedicales.fr › Phénomènes chimiques › Concentration en ions d'hydrogène › Galvani Offset Potential and Constant-pH...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines membranaires › Galvani Offset Potential and Constant-pH...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Simulation numérique › Simulation de dynamique moléculaire › Galvani Offset Potential and Constant-pH...
questionsmedicales.fr › Produits chimiques inorganiques › Composés de l'oxygène › Oxydes › Eau › Galvani Offset Potential and Constant-pH...