Effect of potential binding site overlap to binding of cellulase to cellulose: a two-dimensional simulation.
A computer simulation model for the binding of ligands to a totally anisotropic surface (infinite two-dimensional square lattice) with overlapping binding sites has been developed. The validity of the simulation has been proven by comparison with cases where the correct results are known. The simulation of kinetics shows that when the lattice is close to saturation, the true equilibrium state is reached extremely slowly due to a lot of rearranging of the ligands on the lattice. Based on these findings, the terms 'apparent saturation' and 'apparent maximum coverage' have been introduced and defined. The largest discrepancies between 'apparent maximum coverage' and the theoretically predicted value were observed for ligands of large size and/or irregular shape. As an example, the model has been applied to describe the binding of cellobiohydrolase-I core to Avicel. A formula for calculation of the intrinsic binding constant, maximal binding capacity and specific surface of cellulose from real binding data has been derived.
Institute of Molecular and Cell Biology, University of Tartu, Estonia.
V
V
Sild
J
J
Ståhlberg
G
G
Pettersson
G
G
Johansson
D000327:Adsorption; D001665:Binding Sites; D002480:Cellulase / Q000378:metabolism*; D002482:Cellulose / Q000737:chemistry / Q000378:metabolism*; D043366:Cellulose 1,4-beta-Cellobiosidase; D003198:Computer Simulation; D006026:Glycoside Hydrolases / Q000737:chemistry; D007700:Kinetics; D008433:Mathematics; D011485:Protein Binding; D015203:Reproducibility of Results; D014242:Trichoderma / Q000201:enzymology
D002482:Cellulose; D006026:Glycoside Hydrolases; D002480:Cellulase; D043366:Cellulose 1,4-beta-Cellobiosidase