Evolution of 'ligand-diffusion chreodes' on protein-surface models: a genetic-algorithm study

Chem Biodivers. 2007 Dec;4(12):2766-71. doi: 10.1002/cbdv.200790225.

Abstract

Lattice models have been previously used to model ligand diffusion on protein surfaces. Using such models, it has been shown that the presence of pathways (or 'chreodes') of consecutive residues with certain properties can decrease the number of steps required for the arrival of a ligand at the active site. In this work, we show that, based on a genetic algorithm, ligand-diffusion pathways can evolve on a protein surface, when this surface is selected for shortening the travel length toward the active site. Biological implications of these results are discussed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Diffusion
  • Ligands
  • Models, Biological
  • Proteins / genetics*
  • Proteins / metabolism*
  • Surface Properties

Substances

  • Ligands
  • Proteins