Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein

Elsa F. Henriques, Maria J. Ramos, Christopher A. Reynolds

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

A new approach to the molecular modelling of homologous serine proteases is adopted, by including a set of 21 buried waters known to be preserved in enzymes sharing the primary specificity of trypsin, in the homology modelling of rat submaxillary gland kallikrein. Buried waters - water molecules sequestered from bulk solvent within a protein matrix - appear to be integral conserved components of all serine proteases of known structure and should be incorporated into serine protease models built on the basis of sequence/structural homology to this family. The absence of such waters might induce errors in a force field simulation, favouring the formation of nonexistent hydrogen bonds and locally inaccurate structure. The kallikrein model refinement has led to the conclusion that an additional buried water should be added to the original rigid matrix of 21 conserved water molecules. The structurally preserved protein cavities of such waters validate the modelled structure.

Original languageEnglish
Pages (from-to)547-556
Number of pages10
JournalJournal of Computer-Aided Molecular Design
Volume11
Issue number6
DOIs
Publication statusPublished - 1 Jan 1997
Externally publishedYes

Keywords

  • Homology modelling
  • Molecular dynamics
  • Molecular modelling
  • Protein structure
  • Rat submandibular kallikrein

ASJC Scopus subject areas

  • Drug Discovery
  • Computer Science Applications
  • Physical and Theoretical Chemistry

Fingerprint Dive into the research topics of 'Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein'. Together they form a unique fingerprint.

  • Cite this