Effect of potential binding site overlap to binding of cellulose to cellulose: a two‐dimensional simulation

Abstract

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.

Toward an aggregated understanding of enzymatic hydrolysis of cellulose: Noncomplexed cellulase systems

“…For C. fimi, Gilkes et al (1992) estimate values of 32.9, 39.2, and 27.9 for CenA, the cellulose binding domain of CenA, and Cex, respectively. The catalytic domain of CBH1 is believed to occupy about 48 cellobiose lattices on a totally anisotropic surface (Sild et al, 1996), based on structural information inferred from X-ray crystallography (Divne et al, 1994). The CBM of CBH1 from T. reesei is thought to occupy about 10 cellobiose lattices based on nuclear magnetic resonance data (Kraulis et al, 1989;Reinikainen et al, 1995b).…”

Activity Studies and Crystal Structures of Catalytically Deficient Mutants of Cellobiohydrolase I fromTrichoderma reesei

“…large catalytic domain connected to a small cellulose-binding domain (CBD) via a glycosylated linker peptide. It has been proposed that the two domains interact simultaneously with the cellulose surface, each with different binding specificities, thereby enabling the enzyme to move along the cellulose surface through two-dimensional lateral diffusion (Ståhlberg et al, 1991;Sild et al, 1996).…”

Progress curves

“…The modelling was carried out using a recently developed simulation program [19]. The fibre surface to which the cellulase-shaped ligands were to bind consisted of 80 chains, each containing 120 cellobiose units (average length of the fibres in our experiment), and giving 80ϫ120 elementary binding sites in the layer.…”