A cellular automata model of ligand passage over a protein hydrodynamic landscape.
The subject of ligand passage to an active site on a protein is addressed. Current views on the mechanism and the possible role of surface water are discussed. A theory is presented in which the pattern of hydropathic states of protein surface amino acid side chains is invoked as the influence on the relative hydrophobic effects of nearby water. The theory describes a ligand passage through the hydrodynamic near-surface water which exhibits temporary organized cavities resembling the chreodes introduced by Waddington. The passage of the ligand to the active site is facilitated by this dynamic mechanism. Cellular automata models of preferential directional diffusion through these chreodes support the theory. The theory may be invoked to explain a number of ligand-active site observations and serves as an idea for further studies.
Kier
Lemont B
LB
Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23298, USA.
Cheng
Chao-Kun
CK
Testa
Bernard
B
D000818:Animals; D002477:Cells; D019295:Computational Biology; D004058:Diffusion; D008024:Ligands; D008956:Models, Chemical; D011485:Protein Binding; D011506:Proteins / Q000378:metabolism*; D014867:Water
D008024:Ligands; D011506:Proteins; D014867:Water