Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage et al., 2018). Here, we express three main conc...

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Detalles Bibliográficos
Autores principales: Gapsys, Vytautas, de Groot, Bert L
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2019
Materias:
Structural Biology and Molecular Biophysics
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6586461/
https://www.ncbi.nlm.nih.gov/pubmed/31219782
http://dx.doi.org/10.7554/eLife.44718
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author Gapsys, Vytautas
de Groot, Bert L
author_facet Gapsys, Vytautas
de Groot, Bert L
author_sort Gapsys, Vytautas
collection PubMed
description A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage et al., 2018). Here, we express three main concerns about that study. In addition, we find that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.
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spelling pubmed-65864612019-06-21 Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size' Gapsys, Vytautas de Groot, Bert L eLife Structural Biology and Molecular Biophysics A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage et al., 2018). Here, we express three main concerns about that study. In addition, we find that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed. eLife Sciences Publications, Ltd 2019-06-20 /pmc/articles/PMC6586461/ /pubmed/31219782 http://dx.doi.org/10.7554/eLife.44718 Text en © 2019, Gapsys and de Groot http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Structural Biology and Molecular Biophysics
Gapsys, Vytautas
de Groot, Bert L
Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_full Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_fullStr Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_full_unstemmed Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_short Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_sort comment on 'valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
topic Structural Biology and Molecular Biophysics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6586461/
https://www.ncbi.nlm.nih.gov/pubmed/31219782
http://dx.doi.org/10.7554/eLife.44718
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AT degrootbertl commentonvalidmoleculardynamicssimulationsofhumanhemoglobinrequireasurprisinglylargeboxsize

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