- Previous Article
- Next Article
- Table of Contents
Biochemical and Biophysical Research Communications, Vol.333, No.1, 1-4, 2005
Modeling directed ligand passage toward enzyme active site by a'double cellular automata' model
It is recently proposed that directed passage of ligand on the surface of enzymes may play an important role in the process of enzyme activity, as a result of decreasing the required steps of random walking of the ligand toward the active site. Here, we revisited the approach applied by others, where a cellular automaton is designed to simulate the behavior of a ligand molecule traveling toward the active site of an enzyme. Since a cellular automaton plane is topologically equivalent to a torus surface, we recommended the use of a 'double cellular automata' to model globular proteins. With the boundary conditions applied, our model is topologically identical to a sphere. It was shown that using this model, even fewer steps are needed for a molecule to attend the active site. This assumption can lead to more realistic results in the modeling of surfaces with spherical topology. (c) 2005 Elsevier Inc. All rights reserved.
Keywords:cellular automata;protein surface;perfect enzyme;von Neumann neighborhood;moor neighborhood