Literature DB >> 31219783

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

Krystel El Hage1, Florent Hédin1, Prashant K Gupta1, Markus Meuwly1, Martin Karplus2,3.   

Abstract

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.
© 2019, El Hage et al.

Entities:  

Keywords:  box size; computational biology; hemoglobin; hydrophobic effect; molecular biophysics; molecular dynamics; none; structural biology; systems biology

Mesh:

Substances:

Year:  2019        PMID: 31219783      PMCID: PMC6586459          DOI: 10.7554/eLife.45318

Source DB:  PubMed          Journal:  Elife        ISSN: 2050-084X            Impact factor:   8.140


  15 in total

Review 1.  Interfaces and the driving force of hydrophobic assembly.

Authors:  David Chandler
Journal:  Nature       Date:  2005-09-29       Impact factor: 49.962

2.  Role of the subunit interactions in the conformational transitions in adult human hemoglobin: an explicit solvent molecular dynamics study.

Authors:  Olaniyi K Yusuff; Jonathan O Babalola; Giovanni Bussi; Simone Raugei
Journal:  J Phys Chem B       Date:  2012-08-30       Impact factor: 2.991

3.  Structural Interpretation of Metastable States in Myoglobin-NO.

Authors:  Maksym Soloviov; Akshaya K Das; Markus Meuwly
Journal:  Angew Chem Int Ed Engl       Date:  2016-07-13       Impact factor: 15.336

4.  Extensions of the allosteric model for haemoglobin.

Authors:  S J Edelstein
Journal:  Nature       Date:  1971-03-26       Impact factor: 49.962

5.  HSO3Cl: a prototype molecule for studying OH-stretching overtone induced photodissociation.

Authors:  Juvenal Yosa Reyes; Sebastian Brickel; Oliver T Unke; Tibor Nagy; Markus Meuwly
Journal:  Phys Chem Chem Phys       Date:  2016-02-15       Impact factor: 3.676

6.  Direct determination of protonation states of histidine residues in a 2 A neutron structure of deoxy-human normal adult hemoglobin and implications for the Bohr effect.

Authors:  Andrey Y Kovalevsky; Toshiyuki Chatake; Naoya Shibayama; Sam-Yong Park; Takuya Ishikawa; Marat Mustyakimov; Zoe Fisher; Paul Langan; Yukio Morimoto
Journal:  J Mol Biol       Date:  2010-03-15       Impact factor: 5.469

7.  Dynamics of vibrational overtone excitations of H2SO4, H2SO4-H2O: hydrogen-hopping and photodissociation processes.

Authors:  Yifat Miller; R Benny Gerber
Journal:  J Am Chem Soc       Date:  2006-08-02       Impact factor: 15.419

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

Authors:  Vytautas Gapsys; Bert L de Groot
Journal:  Elife       Date:  2019-06-20       Impact factor: 8.140

9.  Collective dynamics underlying allosteric transitions in hemoglobin.

Authors:  Martin D Vesper; Bert L de Groot
Journal:  PLoS Comput Biol       Date:  2013-09-19       Impact factor: 4.475

10.  Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size.

Authors:  Krystel El Hage; Florent Hédin; Prashant K Gupta; Markus Meuwly; Martin Karplus
Journal:  Elife       Date:  2018-07-12       Impact factor: 8.140

View more
  6 in total

1.  Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics.

Authors:  Yi Zhuang; Nikhil Thota; Stephen Quirk; Rigoberto Hernandez
Journal:  J Chem Theory Comput       Date:  2022-07-13       Impact factor: 6.578

2.  Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.

Authors:  Tamar Schlick; Stephanie Portillo-Ledesma; Christopher G Myers; Lauren Beljak; Justin Chen; Sami Dakhel; Daniel Darling; Sayak Ghosh; Joseph Hall; Mikaeel Jan; Emily Liang; Sera Saju; Mackenzie Vohr; Chris Wu; Yifan Xu; Eva Xue
Journal:  Annu Rev Biophys       Date:  2021-02-19       Impact factor: 12.981

3.  Uncertainty quantification in classical molecular dynamics.

Authors:  Shunzhou Wan; Robert C Sinclair; Peter V Coveney
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2021-03-29       Impact factor: 4.226

4.  Dynamics of camel and human hemoglobin revealed by molecular simulations.

Authors:  Amanat Ali; Soja Saghar Soman; Ranjit Vijayan
Journal:  Sci Rep       Date:  2022-01-07       Impact factor: 4.379

Review 5.  Rapid, accurate, precise and reproducible ligand-protein binding free energy prediction.

Authors:  Shunzhou Wan; Agastya P Bhati; Stefan J Zasada; Peter V Coveney
Journal:  Interface Focus       Date:  2020-10-16       Impact factor: 3.906

6.  On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size.

Authors:  Vytautas Gapsys; Bert L de Groot
Journal:  Elife       Date:  2020-08-19       Impact factor: 8.140

  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.