Mobility-based prediction of hydration structures of protein surfaces

Norbert Jeszenoi, István Horváth, Mónika Bálint, David Van Der Spoel, Csaba Hetényi

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Motivation: Hydration largely determines solubility, aggregation of proteins and influences interactions between proteins and drug molecules. Despite the importance of hydration, structural determination of hydration structure of protein surfaces is still challenging from both experimental and theoretical viewpoints. The precision of experimental measurements is often affected by fluctuations and mobility of water molecules resulting in uncertain assignment of water positions. Results: Our method can utilize mobility as an information source for the prediction of hydration structure. The necessary information can be produced by molecular dynamics simulations accounting for all atomic interactions including water-water contacts. The predictions were validated and tested by comparison to more than 1500 crystallographic water positions in 20 hydrated protein molecules including enzymes of biomedical importance such as cyclin-dependent kinase 2. The agreement with experimental water positions was larger than 80% on average. The predictions can be particularly useful in situations where no or limited experimental knowledge is available on hydration structures of molecular surfaces.

Original languageEnglish
Pages (from-to)1959-1965
Number of pages7
JournalBioinformatics
Volume31
Issue number12
DOIs
Publication statusPublished - Jun 15 2015

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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