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.
Marashi
Sayed-Amir
SA
Department of Biotechnology, Faculty of Science, University of Tehran, Iran.
Behrouzi
Reza
R
D000465:Algorithms; D001185:Artificial Intelligence; D001665:Binding Sites; D003198:Computer Simulation; D004058:Diffusion; D004789:Enzyme Activation; D004798:Enzymes / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D020409:Molecular Motor Proteins / Q000737:chemistry*; D009038:Motion; D046912:Multiprotein Complexes / Q000737:chemistry*; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry*
D004798:Enzymes; D020409:Molecular Motor Proteins; D046912:Multiprotein Complexes; D011506:Proteins