Effect of solvent on protein structure and dynamics

Anshuman Bose Majumdar, In Jung Kim, Hyuntae Na

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Understanding how much solvents influence the structures and dynamics of proteins is important to understand functional mechanisms of solvated proteins. We propose a solvated potential model that approximates the potential energy of a solvated protein by projecting the solvent information into the protein structure. Using the model, we derive three properties of the solvent. First, the influence of the solvent on protein structure and dynamics, mostly by the bulk solvent, decays drastically (near-exponentially) as the distances of the solvent from the protein increase. Using this decay pattern, we suggest the economical size of solvent boxes in molecular dynamics simulations. Second, the hydration shell regulates the protein dynamics by effecting extra interactions within the protein structure. Lastly, the lowest frequency modes are determined mostly by protein structures.

Original languageEnglish (US)
Article number036006
JournalPhysical Biology
Volume17
Issue number3
DOIs
StatePublished - May 2020

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Structural Biology
  • Molecular Biology
  • Cell Biology

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