Combining Simulation and Spectroscopy to Determine the Structure and Orientation of a Carbohydrate Binding Module (CBM) Inspired Model Peptide on Cellulose

Interfacial processes, such as the enzymatic conversion of an insoluble polysaccharide at the solid-liquid interface, are critically important to the design of new systems to convert renewable resources into green fuels and chemicals. Despite this fact, we often lack a molecularly detailed understanding of these interfaces that hinders the rational design of new and/or improved biocatalytic systems. Atomistic simulations of biomolecular adsorption using state-of-the-art multiscale molecular modeling tools have strong potential to combine with advanced, surface-specific spectroscopy to elucidate structural and mechanistic details at the interface. To this end, enhanced sampling methods based on the metadynamics family of methods have been combined with experimental data from sum frequency generation spectroscopy (SFG) to probe the equilibrium structure(s) and preferred orientation(s) of a 14-residue peptide fragment inspired by the carbohydrate binding module (CBM) of a cellulase. Experimental SFG data indicates the CBM fragment adsorbs to the cellulose surface and aligns along the fibers in a distinct orientation/conformation. We use a variety of molecular simulations to provide molecular level insight to this observation and add additional detail beyond the amide I backbone spectra, thus providing new mechanistic insights regarding biomass conversion. Additionally, simulation results are used to determine the energetic penalties for binding in alternate orientations, and to identify the specific reasons for the observed behaviors. In a broader sense, this integrated approach of combining computational methods with experiments aims to determine the role of the surface in modulating biomolecular structure, thereby permitting the rational design of new biocatalytic approaches.