Browsing by Author "Lin, Yuchun"

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Endoglucanase Peripheral Loops Facilitate Complexation of Glucan Chains on Cellulose via Adaptive Coupling to the Emergent Substrate Structures
(2013-09-19)
Lin, Yuchun
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Beckham, Gregg T.
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Himmel, Michael E.
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Crowley, Michael F.
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Chu, Jhih-Wei
We examine how the catalytic domain of a glycoside hydrolase family 7 endoglucanase catalytic domain (Cel7B CD) facilitates complexation of cellulose chains from a crystal surface. With direct relevance to the science of biofuel production, this problem also represents a model system of biopolymer processing by proteins in Nature. Interactions of Cel7B CD with a cellulose microfibril along different paths of complexation are characterized by mapping the atomistic fluctuations recorded in free-energy simulations onto the parameters of a coarse-grain model. The resulting patterns of protein-biopolymer couplings also uncover the sequence signatures of the enzyme in peeling off glucan chains from the microfibril substrate. We show that the semiopen active site of Cel7B CD exhibits similar barriers and free energies of complexation over two distinct routes; namely, scooping of a chain into the active-site cleft and threading from the chain end into the channel. On the other hand, the complexation energetics strongly depends on the surface packing of the targeted chain and the resulting interaction sites with the enzyme. A revealed principle is that Cel7B CD facilitates cellulose deconstruction via adaptive coupling to the emergent substrate. The flexible, peripheral segments of the protein outside of the active-site cleft are able to accommodate the varying features of cellulose along the simulated paths of complexation. The general strategy of linking physics-based molecular interactions to protein sequence could also be helpful in elucidating how other protein machines process biopolymers.
Importance of Internal Porosity for Glucan Adsorption in Mesoporous Carbon Materials
(2015-07-07)
Chung, Po-Wen
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Charmot, Alexandre
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Click, Timothy
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Lin, Yuchun
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Bae, YounJue
To better understand the adsorption of long-chain poly(1 -> 4)beta-D-glucans on carbon surfaces as well as interactions responsible for this adsorption, we use a comparative study involving mesoporous carbon silica composite materials that have been etched to varying degrees and all-atom molecular dynamics simulations. The materials synthesized as part of this etching study consist of an as-synthesized composite material (MCN-MSN), MCN-MSN-0.5 (composite materials consisting of 50% carbon by mass), MCN-MSN-0.3 (composite materials consisting of 70% carbon by mass), and MCN, in which silica etching was conducted using an aqueous ethanolic solution of either NaOH or HF. Data for the adsorption of long-chain glucans to these materials from concentrated aqueous HCl (37 wt %) solution demonstrate a direct relationship between the amount of beta-glu adsorption and the magnitude of exposed carbon mesopore surface area, which systematically increases and is also accompanied by an increase in the mesopore size during silica etching. This demonstrates beta-glu adsorption as occurring on internal carbon mesopores rather than exclusively on the external carbon surface. These experimental data on adsorption were corroborated by molecular dynamics (MD) simulations of beta-glu adsorption to a graphene bilayer separated by a distance of 3.2 nm, chosen to correspond to the carbon mesopore diameter of the experimental system. Simulation results using a variety of beta-glu solvent systems demonstrate the rapid adsorption of a beta-glu strand on the graphitic carbon surface via axial coupling and are consistent with experimentally observed trends in fast adsorption kinetics. Solvent-mediated effects such as small-scale hydrophobicity and preferential interactions with ions are shown to play important roles in modulating glucan adsorption to carbon surfaces, whereas experimental data on hydrophobically modified silica demonstrate that hydrophobicity in and of itself is insufficient to cause beta-glu adsorption from concentrated aqueous HCl solution.