Design of Compact Biomimetic Cellulose Binding Peptides as Carriers for Cellulose Catalytic Degradation

Abstract

The conversion of biomass into biofuels can reduce the strategic vulnerability of petroleum-based systems and at the same time have a positive effect on global climate issues. Lignocellulose is the cheapest and most abundant source of biomass and consequently has been widely considered as a source for liquid fuel. However, despite ongoing efforts, cellulosic biofuels are still far from commercial realization, one of the major bottlenecks being the hydrolysis of cellulose into simpler sugars. Inspired by the structural and functional modularity of cellulases used by many organisms for the breakdown of cellulose, we propose to mimic the cellulose binding domain (CBD) and the catalytic domain of these proteins by small molecular entities. Multiple copies of these mimics could subsequently be tethered together to enhance hydrolytic activity. In this work, we take the first step toward achieving this goal by applying computational approaches to the design of efficient, cost-effective mimetics of the CBD. The design is based on low molecular weight peptides that are amenable to large-scale production. We provide an optimized design of four short (i.e., ∼18 residues) peptide mimetics based on the three-dimensional structure of a known CBD and demonstrate that some of these peptides bind cellulose as well as or better than the full CBD. The structures of these peptides were studied by circular dichroism and their interactions with cellulose by solid phase NMR. Finally, we present a computational strategy for predicting CBD/peptide-cellulose binding free energies and demonstrate its ability to provide values in good agreement with experimental data. Using this computational model, we have also studied the dissociation pathway of the CBDs/peptides from the surface of cellulose.

Interaction of carbohydrate-binding modules with poly(ethylene terephthalate)

“…Subsequently, three candidates were subjected to molecular dynamics (MD) simulations trying to reveal their mode of action and to correlate the experimentally determined affinity with the calculated models. Several recent studies described MD methods to examine the interactions of CBM1 from Trichoderma reesei with cellulose, which is a glucose-based polysaccharide (Nimlos et al 2007 ; Beckham et al 2010 ; Nimlos et al 2012 ; Shiiba et al 2013 ; Khazanov et al 2016 ). There are, however, no atomistic MD studies of CBM interactions with other polymers like the synthetic PET.…”

Antibacterial, Cytocompatible, Sustainably Sourced: Cellulose Membranes with Bifunctional Peptides for Advanced Wound Dressings

“…[ 18,40 ] Binding to cellulose strongly depends on the specific amino acid sequence, and various research approaches resulted in the identification of shorter units, the CBP. [ 25,41 ] The affinity is governed by combined noncovalent interactions that involve, e.g., binding of tyrosine to single cellulose polymer chains via CH/π‐stacking‐, hydrogen bonding, and hydrophobic interactions with the glucose rings. [ 25,42 ] These interactions in concert facilitate the site‐directed immobilization of CBPs on cellulose substrates with high selectivity and (bio‐)affinity constants as high as 10 5 m −1 .…”

A Review on the Modification of Cellulose and Its Applications

“…Biodegradable ILs will be developed for dissolving cellulose in order to be helpful in various applications [ 140 ]. To avoid undesirable byproducts, it is vital to watch for reactions and intervene quickly, [ 141 , 142 ] including the ability to take rapid action to prevent the development of byproducts and the avoidance of sample pretreatment.…”