Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks

Vilhelm Ekberg, Marley L. Samways, Majda Misini Ignjatović, Jonathan W. Essex, Ulf Ryde

Research output: Contribution to journalArticlepeer-review

Abstract

Water molecules play important roles in all biochemical processes. Therefore, it is of key importance to obtain information of the structure, dynamics, and thermodynamics of water molecules around proteins. Numerous computational methods have been suggested with this aim. In this study, we compare the performance of conventional and grand-canonical Monte Carlo (GCMC) molecular dynamics (MD) simulations to sample the water structure, as well GCMC and grid-based inhomogeneous solvation theory (GIST) to describe the energetics of the water network. They are evaluated on two proteins: the buried ligand-binding site of a ferritin dimer and the solvent-exposed binding site of galectin-3. We show that GCMC/MD simulations significantly speed up the sampling and equilibration of water molecules in the buried binding site, thereby making the results more similar for simulations started from different states. Both GCMC/MD and conventional MD reproduce crystal-water molecules reasonably for the buried binding site. GIST analyses are normally based on restrained MD simulations. This improves the precision of the calculated energies, but the restraints also significantly affect both absolute and relative energies. Solvation free energies for individual water molecules calculated with and without restraints show a good correlation, but with large quantitative differences. Finally, we note that the solvation free energies calculated with GIST are ∼5 times larger than those estimated by GCMC owing to differences in the reference state.
Original languageEnglish
Pages (from-to)247-259
Number of pages13
JournalACS Physical Chemistry Au
Volume2
Issue number3
DOIs
Publication statusPublished - 2022

Subject classification (UKÄ)

  • Theoretical Chemistry

Free keywords

  • protein solvation
  • water networks
  • molecular dynamics simulations
  • grand-canonical Monte Carlo simulations
  • grid-based inhomogeneous solvation theory

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