Molecules (Jul 2019)

Topological Water Network Analysis Around Amino Acids

  • Kwang-Eun Choi,
  • Eunkyoung Chae,
  • Anand Balupuri,
  • Hye Ree Yoon,
  • Nam Sook Kang

DOI
https://doi.org/10.3390/molecules24142653
Journal volume & issue
Vol. 24, no. 14
p. 2653

Abstract

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Water molecules play a key role in protein stability, folding, function and ligand binding. Protein hydration has been studied using free energy perturbation algorithms. However, the study of protein hydration without free energy calculation is also an active field of research. Accordingly, topological water network (TWN) analysis has been carried out instead of free energy calculation in the present work to investigate hydration of proteins. Water networks around 20 amino acids in the aqueous solution were explored through molecular dynamics (MD) simulations. These simulation results were compared with experimental observations. Water molecules from the protein data bank structures showed TWN patterns similar to MD simulations. This work revealed that TWNs are effected by the surrounding environment. TWNs could provide valuable clues about the environment around amino acid residues in the proteins. The findings from this study could be exploited for TWN-based drug discovery and development.

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