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

Vytautas GapsysBert L de Groot
Published in: eLife (2019)
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.
Keyphrases
  • molecular dynamics
  • molecular dynamics simulations
  • binding protein
  • transcription factor
  • density functional theory
  • endothelial cells
  • molecular docking
  • red blood cell
  • ionic liquid
  • solar cells