Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

We recently reported that molecular dynamics simulations for hemoglobin require a surprisingly large box size to stabilize the T(0) state relative to R(0), as observed in experiments (El Hage et al., 2018). Gapsys and de Groot have commented on this work but do not provide convincing evidence that t...

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Main Authors:	Krystel El Hage, Florent Hédin, Prashant K Gupta, Markus Meuwly, Martin Karplus
Format:	Article
Language:	English
Published:	eLife Sciences Publications Ltd 2019-06-01
Series:	eLife
Subjects:	hemoglobin molecular dynamics hydrophobic effect box size
Online Access:	https://elifesciences.org/articles/45318

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record_format	Article
spelling	doaj-cf0ccba87d8f4b51a0db52174f9675af2021-05-05T17:42:19ZengeLife Sciences Publications LtdeLife2050-084X2019-06-01810.7554/eLife.45318Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'Krystel El Hage0https://orcid.org/0000-0003-4837-3888Florent Hédin1https://orcid.org/0000-0001-6341-7557Prashant K Gupta2https://orcid.org/0000-0002-4792-7538Markus Meuwly3https://orcid.org/0000-0001-7930-8806Martin Karplus4Department of Chemistry, University of Basel, Basel, SwitzerlandDepartment of Chemistry, University of Basel, Basel, SwitzerlandDepartment of Chemistry, University of Basel, Basel, SwitzerlandDepartment of Chemistry, University of Basel, Basel, SwitzerlandDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, United States; Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, Strasbourg, FranceWe recently reported that molecular dynamics simulations for hemoglobin require a surprisingly large box size to stabilize the T(0) state relative to R(0), as observed in experiments (El Hage et al., 2018). Gapsys and de Groot have commented on this work but do not provide convincing evidence that the conclusions of El Hage et al., 2018 are incorrect. Here we respond to these concerns, argue that our original conclusions remain valid, and raise our own concerns about some of the results reported in the comment by Gapsys and de Groot that require clarification.https://elifesciences.org/articles/45318hemoglobinmolecular dynamicshydrophobic effectbox size
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Krystel El Hage Florent Hédin Prashant K Gupta Markus Meuwly Martin Karplus
spellingShingle	Krystel El Hage Florent Hédin Prashant K Gupta Markus Meuwly Martin Karplus Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size' eLife hemoglobin molecular dynamics hydrophobic effect box size
author_facet	Krystel El Hage Florent Hédin Prashant K Gupta Markus Meuwly Martin Karplus
author_sort	Krystel El Hage
title	Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_short	Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_full	Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_fullStr	Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_full_unstemmed	Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
title_sort	response to comment on 'valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
publisher	eLife Sciences Publications Ltd
series	eLife
issn	2050-084X
publishDate	2019-06-01
description	We recently reported that molecular dynamics simulations for hemoglobin require a surprisingly large box size to stabilize the T(0) state relative to R(0), as observed in experiments (El Hage et al., 2018). Gapsys and de Groot have commented on this work but do not provide convincing evidence that the conclusions of El Hage et al., 2018 are incorrect. Here we respond to these concerns, argue that our original conclusions remain valid, and raise our own concerns about some of the results reported in the comment by Gapsys and de Groot that require clarification.
topic	hemoglobin molecular dynamics hydrophobic effect box size
url	https://elifesciences.org/articles/45318
work_keys_str_mv	AT krystelelhage responsetocommentonvalidmoleculardynamicssimulationsofhumanhemoglobinrequireasurprisinglylargeboxsize AT florenthedin responsetocommentonvalidmoleculardynamicssimulationsofhumanhemoglobinrequireasurprisinglylargeboxsize AT prashantkgupta responsetocommentonvalidmoleculardynamicssimulationsofhumanhemoglobinrequireasurprisinglylargeboxsize AT markusmeuwly responsetocommentonvalidmoleculardynamicssimulationsofhumanhemoglobinrequireasurprisinglylargeboxsize AT martinkarplus responsetocommentonvalidmoleculardynamicssimulationsofhumanhemoglobinrequireasurprisinglylargeboxsize
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Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

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