Peptide Recognition Capabilities of Cellulose in Molecular Dynamics Simulations

Abstract

Knowing the amino acid discriminating capacity of the surface of cellulose can be valuable information toward the rational design and re-engineering of the cellulosome in order to improve its catalytic properties. This aim can be achieved by the determination of the binding free energies of amino acids in molecular dynamics simulations. Conventional simulations do not always allow for sufficient sampling of the configuration space, especially in a system where large energy barriers occur. A better sampling can be obtained by replica exchange molecular dynamics (REMD). Here, we use REMD combined with umbrella sampling to determine the potential of the mean force for amino acids, analogues of their side chains, dipeptides, and tripeptides for the interactions with the (100) face of the crystalline cellulose Iβ. We also use REMD to characterize the adsorption dynamics of a small protein, tryptophan cage. Our results show that all 20 standard amino acids adsorb on the surface of cellulose with binding energie...