Evolution of 'ligand-diffusion chreodes' on protein-surface models: a genetic-algorithm study.
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.
Marashi
Sayed-Amir
SA
Department of Biotechnology, University College of Science, University of Tehran, Enghelab Avenue, Tehran, Iran. marashie@khayam.ut.ac.ir
Kargar
Mehdi
M
Katanforoush
Ali
A
Abolhassani
Hassan
H
Sadeghi
Mehdi
M
D000465:Algorithms; D004058:Diffusion; D008024:Ligands; D008954:Models, Biological; D011506:Proteins / Q000235:genetics* / Q000378:metabolism*; D013499:Surface Properties
D008024:Ligands; D011506:Proteins