Hydrogen-bond patterns in the hydration structure of a protein

Tsuyoshi Yokomizo, Masayoshi Nakasako, Toshimasa Yamazaki, Heizaburo Shindo, Junich Higo

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Hydrogen-bond (H-bond) patterns of water molecules around a small protein molecule were studied with a molecular dynamics simulation. By using a coordinate system fixed on the protein, time-averaged H-bond patterns were calculated from the trajectory. Coherent H-bond patterns appeared only near the protein surface, in spite that the H-bond ability near the protein surface was the same as that in bulk-water regions. Thus, the patterns were consequence of highly preferential H-bond formation between specific sites on the protein surface and water molecules. Furthermore, the sites characterized by the coherent H-bond patterns displayed large solvent densities and strong solvent site-dipoles.

Original languageEnglish
Pages (from-to)332-336
Number of pages5
JournalChemical Physics Letters
Volume401
Issue number4-6
DOIs
Publication statusPublished - 2005 Jan 11

Fingerprint

Hydration
hydration
Hydrogen bonds
hydrogen bonds
proteins
Membrane Proteins
Proteins
Molecules
Water
water
molecules
Molecular dynamics
Trajectories
trajectories
dipoles
molecular dynamics
Computer simulation
simulation

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Spectroscopy
  • Atomic and Molecular Physics, and Optics
  • Surfaces and Interfaces
  • Condensed Matter Physics

Cite this

Hydrogen-bond patterns in the hydration structure of a protein. / Yokomizo, Tsuyoshi; Nakasako, Masayoshi; Yamazaki, Toshimasa; Shindo, Heizaburo; Higo, Junich.

In: Chemical Physics Letters, Vol. 401, No. 4-6, 11.01.2005, p. 332-336.

Research output: Contribution to journalArticle

Yokomizo, Tsuyoshi ; Nakasako, Masayoshi ; Yamazaki, Toshimasa ; Shindo, Heizaburo ; Higo, Junich. / Hydrogen-bond patterns in the hydration structure of a protein. In: Chemical Physics Letters. 2005 ; Vol. 401, No. 4-6. pp. 332-336.
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