Paper Citing NAMD - Abstract
Lin, Yuchun; Silvestre-Ryan, Jordi; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.; Chu, Jhih-Wei
Protein Allostery at the Solid-Liquid Interface: Endoglucanase Attachment to Cellulose Affects Glucan Clenching in the Binding Cleft
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:16617-16624, OCT 19 2011
At phase boundaries, physical activities of enzymes such as substrate complexation play critical roles in driving biocatalysis. A prominent example is the cellulase cocktails secreted by fungi and bacteria for deconstructing crystalline cellulose in biomass into soluble sugars. At interfaces, molecular mechanisms of the physical steps in biocatalysis remain elusive due to the difficulties of characterizing protein action with high temporal and spatial resolution. Here, we focus on endoglucanase I (Cel7B) from the fungus Trichoderma reesei that hydrolyzes glycosidic bonds on cellulose randomly. We employ all-atom molecular dynamics (MD) simulations to elucidate the interactions of the catalytic domain (CD) of Cel7B with a cellulose microfibril before and after complexing a glucan chain in the binding cleft. The calculated mechanical coupling networks in Cel7B-glucan and Cel7B-microfibril complexes reveal a previously unresolved allosteric coupling at the solid liquid interface: attachment of the Cel7B-CD to the cellulose surface affects glucan chain clenching in the binding cleft. Alternative loop segments of the Cel7B-CD were found to affix to intact or defective surface structures on the microfibril, depending on the complexation state. From a multiple sequence alignment, residues in surface-affixing segments show strong conservation, highlighting the functional importance of the physical activities that they facilitate. Surface-affixing residues also demonstrate significant sequence correlation with active-site residues, revealing the functional connection between complexation and hydrolysis. Analysis of the Cel7B-CD exemplifies that the mechanical coupling networks calculated from atomistic MD simulations can be used to capture the conservation and correlation in sequence alignment.
