No abstract

Cytophaga hutchinsonii is a Gram-negative gliding bacterium which can efficiently degrade crystalline cellulose by an unknown strategy. Genomic analysis suggests the C. hutchinsonii genome lacks homologs to an obvious exoglucanase that previously seemed essential for cellulose degradation. One of the putative endoglucanases, CHU_2103, was successfully expressed in Escherichia coli JM109 and identified as a processive endoglucanase with transglycosylation activity. It could hydrolyze carboxymethyl cellulose (CMC) into cellodextrins and rapidly decrease the viscosity of CMC. When regenerated amorphous cellulose (RAC) was degraded by CHU_2103, the ratio of the soluble to insoluble reducing sugars was 3.72 after 3 h with cellobiose and cellotriose as the main products, indicating that CHU_2103 was a processive endoglucanase. CHU_2103 could degrade cellodextrins of degree of polymerization ≥3. It hydrolyzed p-nitrophenyl β-D-cellodextrins by cutting glucose or cellobiose from the non-reducing end. Meanwhile, some larger-molecular-weight cellodextrins could be detected, indicating it also had transglycosylation activity. Without carbohydrate-binding module (CBM), CHU_2103 could bind to crystalline cellulose and acted processively on it. Site-directed mutation of CHU_2103 demonstrated that the conserved aromatic amino acid W197 in the catalytic domain was essential not only for its processive activity, but also its cellulose binding ability.

No abstract

Coulomb interaction, following an inverse-square force-law, quantifies the amount of force between two stationary and electrically charged particles. The long-range nature of Coulomb interactions poses a major challenge to molecular dynamics simulations, which are major tools for problems at the nano-/micro-scale. Various algorithms are developed to calculate the pairwise Coulomb interactions to a linear scale, but poor scalability limits the size of simulated systems. Here, we use an efficient molecular dynamics algorithm with the random batch Ewald method on all-atom systems where the complete Fourier components in the Coulomb interaction are replaced by randomly selected mini-batches. By simulating the N-body systems up to 108 particles using 10 000 central processing unit cores, we show that this algorithm furnishes O(N) complexity, almost perfect scalability, and an order of magnitude faster computational speed when compared to the existing state-of-the-art algorithms. Further examinations of our algorithm on distinct systems, including pure water, a micro-phase separated electrolyte, and a protein solution, demonstrate that the spatiotemporal information on all time and length scales investigated and thermodynamic quantities derived from our algorithm are in perfect agreement with those obtained from the existing algorithms. Therefore, our algorithm provides a promising solution on scalability of computing the Coulomb interaction. It is particularly useful and cost-effective to simulate ultra-large systems, which is either impossible or very costly to conduct using existing algorithms, and thus will be beneficial to a broad range of problems at nano-/micro-scales.

An experimental study of cellobiose inhibition in cellulose hydrolysis by synergism of cellobiohydrolyse I and endoglucanase I is presented. Cellobiose is the structural unit of cellulose molecules and also the main product in enzymatic hydrolysis of cellulose. It has been identified that cellobiose can strongly inhibit hydrolysis reaction of cellulase, whereas it has no effect on the adsorption of cellulase on cellulose surface. The experimental data of FT-IR spectra, fluorescence spectrum and circular dichroism suggested that cellobiose can be combined with tryptophan residue located near the active site of cellobiohydrolase and then form steric hindrance, which prevents cellulose molecule chains from diffusing into active site of cellulase. In addition, the molecular conformation of cellobiohydrolase changes after cellobiose binding, which also causes most of the non-productive adsorption. Under these conditions, microfibrils cannot be separated from cellulose chains, thus further hydrolysis of cellulose can hardly proceed.