Application of empirical hydration distribution functions around polar atoms for assessing hydration structures of proteins

Daisuke Matsuoka, Masayoshi Nakasako

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

To quantitatively characterize hydrogen-bond geometry in local hydration structures of proteins, we constructed a set of empirical hydration distribution functions (EHDFs) around polar protein atoms in the main and side chains of 11 types of hydrophilic amino acids (D. Matsuoka, M. Nakasako, Journal of Physical Chemistry B 113 (2009) 11274). The functions are the ensemble average of possible hydration patterns around the polar atoms, and describe the anisotropic deviations from ideal hydrogen bond geometry. In addition, we defined probability distribution function of hydration water molecules (PDFH) over the hydrophilic surface of a protein as the sum of EHDFs of solvent accessible polar protein atoms. The functions envelop most of hydration sites identified in crystal structures of proteins (D. Matsuoka, M. Nakasako, Journal of Physical Chemistry B 114 (2010) 4652). Here we propose the application of EHDFs and PDFHs for assessing crystallographically identified hydration structures of proteins. First, hydration water molecules are classified with respect to the geometry in hydrogen bonds in referring EHDFs. Difference Fourier electron density map weighted by PDFH of protein is proposed to identify easily density peaks as candidates of hydration water molecules. A computer program implementing those ideas was developed and used for assessing hydration structures of proteins.

Original languageEnglish
Pages (from-to)59-64
Number of pages6
JournalChemical Physics
Volume419
DOIs
Publication statusPublished - 2013 Jan 1

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Keywords

  • Hydration structure
  • Knowledge-based method
  • Protein hydration
  • X-ray crystallography

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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