We present a coarse-grain (CG) simulation model for aqueous solutions of β-d-glucose, cellobiose, and cellotetraose, based on atomistic simulation data for each system. In the model, three spherical beads are used to represent glucose, and a single bead is used to represent water. For glucose, the force field is calculated using force matching by minimizing the sum of the square differences between forces calculated from atomistic and CG simulations. For cellobiose and cellotetraose, we use a hybrid method where the nonbonded interactions are obtained using force matching and the bonded interactions are obtained using Boltzmann inversion. We demonstrate excellent agreement in the structural properties between the atomistic simulations and the CG simulations. This model represents the first step in developing a CG force field for cellulose, as it is of significant interest to study cellulose behavior at much longer time and length scales relative to atomistic simulations.
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Genes (Basel)
September 2024
Leibniz Institute, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany.
This study aims to evaluate the in silico genomic characteristics of five species of the genus : , , , , and , with a view to their application in therapeutic research. The 16S rRNA comparison indicated that these species were phylogenetically distinct. Pairwise comparisons of digital DNA-DNA hybridization (dDDH) and OrthoANI values between these studied type strains indicated that dDDH values were below 62.
View Article and Find Full Text PDFInt J Biol Macromol
August 2024
Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza 2, Milano 20126, Italy.
Glycoside hydrolases (GHs) are pivotal in the hydrolysis of the glycosidic bonds of sugars, which are the main carbon and energy sources. The genome of Marinomonas sp. ef1, an Antarctic bacterium, contains three GHs belonging to family 3.
View Article and Find Full Text PDFAnim Biosci
September 2024
Jilin Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
Objective: This study aimed to identify and characterize a novel endo-β-glucanase, IDSGLUC9-4, from the rumen metatranscriptome of Hu sheep.
Methods: A novel endo-β-glucanase, IDSGLUC9-4, was heterologously expressed in Escherichia coli and biochemically characterized. The optimal temperature and pH of recombinant IDSGLUC9-4 were determined.
Int J Biol Macromol
January 2024
College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310021, China.
A novel acidophilic GH5 β-1,4-endoglucanase (TaCel12) from Trichoderma asperellum ND-1 was efficiently expressed in Pichia pastoris (a 1.5-fold increase). Deglycosylated TaCel12 migrated as a single band (26.
View Article and Find Full Text PDFCarbohydr Polym
April 2024
Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil. Electronic address:
Carbohydrate-active enzymes from the glycoside hydrolase family 9 (GH9) play a key role in processing lignocellulosic biomass. Although the structural features of some GH9 enzymes are known, the molecular mechanisms that drive their interactions with cellulosic substrates remain unclear. To investigate the molecular mechanisms that the two-domain Bacillus licheniformis BlCel9A enzyme utilizes to depolymerize cellulosic substrates, we used a combination of biochemical assays, X-ray crystallography, small-angle X-ray scattering, and molecular dynamics simulations.
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