In silico characterization of the GH5-cellulase family from uncultured microorganisms: physicochemical and structural studies

Abstract

Background Hydrolysis of cellulose-based biomass by cellulases produce fermented sugar for making biofuels, such as bioethanol. Cellulases hydrolyze the β-1,4-glycosidic linkage of cellulose and can be obtained from cultured and uncultured microorganisms. Uncultured microorganisms are a source for exploring novel cellulase genes through the metagenomic approach. Metagenomics concerns the extraction, cloning, and analysis of the entire genetic complement of a habitat without cultivating microbes. The glycoside hydrolase 5 family (GH5) is a cellulase family, as the largest group of glycoside hydrolases. Numerous variants of GH5-cellulase family have been identified through the metagenomic approach, including CelGH5 in this study. University-CoE-Research Center for Biomolecule Engineering, Universitas Airlangga successfully isolated CelGH5 from waste decomposition of oil palm empty fruit bunches (OPEFB) soil by metagenomics approach. The properties and structural characteristics of GH5-cellulases from uncultured microorganisms can be studied using computational tools and software. Results The GH5-cellulase family from uncultured microorganisms was characterized using standard computational-based tools. The amino acid sequences and 3D-protein structures were retrieved from the GenBank Database and Protein Data Bank. The physicochemical analysis revealed the sequence length was roughly 332–751 amino acids, with the molecular weight range around 37–83 kDa, dominantly negative charges with pI values below 7. Alanine was the most abundant amino acid making up the GH5-cellulase family and the percentage of hydrophobic amino acids was more than hydrophilic. Interestingly, ten endopeptidases with the highest average number of cleavage sites were found. Another uniqueness demonstrated that there was also a difference in stability between in silico and wet lab. The II values indicated CelGH5 and ACA61162.1 as unstable enzymes, while the wet lab showed they were stable at broad pH range. The program of SOPMA, PDBsum, ProSA, and SAVES provided the secondary and tertiary structure analysis. The predominant secondary structure was the random coil, and tertiary structure has fulfilled the structure quality of QMEAN4, ERRAT, Ramachandran plot, and Z score. Conclusion This study can afford the new insights about the physicochemical and structural properties of the GH5-cellulase family from uncultured microorganisms. Furthermore, in silico analysis could be valuable in selecting a highly efficient cellulases for enhanced enzyme production.

Understanding Nanocellulose–Water Interactions: Turning a Detriment into an Asset

“…Schematic summary of the role of water in nanocellulose production. Water serves as (a) reagent and (b) swelling agent, (c) an essential medium for tertiary structures of enzymes used for nanocellulose production, and (d) medium in the hydrolysis reaction, (a) Adapted with permission from ref . Copyright 2011 John Wiley and Sons.…”

“…Copyright 2021 Elsevier. (c) Adapted from ref under the terms of CC-BY 4.0. Copyright 2021 Springer Nature.…”

Impact of Synergy Partner Cel7B on Cel7A Binding Rates: Insights from Single-Molecule Data

“…One of the native cysteines in the enzyme core and one in the CBM were exposed to the solvent (see Figure S7), so, in principle, the sample of mutant Cel7A used in our experiments contained enzymes labeled on a native cysteine, the mutant cysteine, or both. However, the formation of the disulfide bridges by the cysteine residues is known to be critical for the enzyme’s activity. − Therefore, the labeling of the native cysteines was expected to lead to Cel7A with impaired functionality so that Cel7A interacts weakly with the cellulose. In this work, the purification protocol based on cellulose ensured that any enzymes that were made inactive following native cysteine labeling were removed.…”

In silico Prediction and Analysis of Autophagy Related Gene-5 Interacting Proteins and their Physicochemical Features

“…Leucine also contributes to protein thermostability nonetheless, serine is investigated to be predominantly synthesized in astrocytes and not in neurons, indicating that it is an essential amino acid for neurons [30]. ATG5 interacting protein negative charges (-R) were calculated using the aspartic and glutamic acid content, while their positive charges (+R) were calculated using the arginine and lysine content by ExPASY ProtParam tool.…”