Biocatalysis: Exploring and Designing Biocatalysts for Molecular Synthesis, and DNA/Protein Bio-Macromolecule Modifications

A special issue of Catalysts (ISSN 2073-4344). This special issue belongs to the section "Biocatalysis".

Deadline for manuscript submissions: closed (20 January 2023) | Viewed by 3076

Special Issue Editors


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Guest Editor
Institute of Biological Chemistry, Academia Sinica, Taipei City, Taiwan
Interests: biocatalysis; expanding genetic codes; protein post-translational modifications; protein chemistry; novel enzyme design for protein modifications

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Guest Editor
School of Chemistry, Institute of Science, Suranaree University of Technology, Chai Mongkhon, Tailand
Interests: enzymology; metabolic engineering of E. coli and biocatalyst development for chemical production

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Guest Editor
New England Biolabs, Ipswich, MA, USA
Interests: DNA modification; nucleic acid chemistry; protein chemistry; nucleic acid enzymes

Special Issue Information

Dear Colleagues,

Biocatalysis carried out by protein catalyst (i.e., enzyme) has proven its great synthetic advantages of superb selectivity and mild processing conditions in the production of valuable chemicals and secondary metabolites as well as biologically significant macromolecules such as proteins with specific post-translational modifications and nucleic acids with specific epigenetic markers. To expand the biocatalytic scope of an arbitrary enzyme for desirable applications, enzymes often require engineering to achieve the application goals, where the engineering process could be conducted by rational design, directed evolution, or a combination of both. In addition, recent developments in biocatalysis have moved forward to implement protein scaffold design in order to explore new chemistry of catalysis on previously unachievable substrate targets. Engineered enzymes could be applied in in vitro molecular synthesis and in vivo production  via the implementation of metabolic engineering strategy. Furthermore, because enzymatic functional studies exploring the regulatory mechanisms they exert via protein post-transcriptional and post-translational modifications (PTMs) have advanced enormously, the biocatalytic modification of target proteins has become possible. Therefore, combining new enzyme chemistry in PTM enzyme and protein scaffolds, and tool development for site-specific drug loading onto therapeutic antibodies is worth exploring. Similarly, as nucleic acids have recently emerged as attractive reagents for potential therapeutic applications, biocatalytic process studies allowing the production of DNA or RNA uniformly with defined compositions and base modifications for better stability and efficacy are extremely valuable. In this Special Issue, we are seeking to explore the realm of studies at the intersection between novel enzyme design for new biocatalytic functions to process medically relevant small-molecule natural products, as well as proteins and nucleic acid macromolecules. We welcome reviews and original research articles that are related to new chemical reactions catalyzed by evolved enzymes that can catalyze chemical transformation or modification on small molecules, proteins, or nucleic acids.

Dr. Yane-Shih Wang
Dr. Rung-Yi Lai
Dr. Yan-Jiun Lee
Guest Editors

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Keywords

  • biocatalyst
  • enzyme
  • protein engineering
  • protein design
  • directed evolution
  • novel chemistry
  • protein modification
  • nucleic acid modification

Published Papers (1 paper)

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Research

20 pages, 3909 KiB  
Article
Systematic Functional and Computational Analysis of Glucose-Binding Residues in Glycoside Hydrolase Family GH116
by Meng Huang, Salila Pengthaisong, Ratana Charoenwattanasatien, Natechanok Thinkumrob, Jitrayut Jitonnom and James R. Ketudat Cairns
Catalysts 2022, 12(3), 343; https://doi.org/10.3390/catal12030343 - 17 Mar 2022
Cited by 7 | Viewed by 2325
Abstract
Glycoside hydrolases (GH) bind tightly to the sugar moiety at the glycosidic bond being hydrolyzed to stabilize its transition state conformation. We endeavored to assess the importance of glucose-binding residues in GH family 116 (GH116) β-glucosidases, which include human β-glucosylceramidase 2 (GBA2), by [...] Read more.
Glycoside hydrolases (GH) bind tightly to the sugar moiety at the glycosidic bond being hydrolyzed to stabilize its transition state conformation. We endeavored to assess the importance of glucose-binding residues in GH family 116 (GH116) β-glucosidases, which include human β-glucosylceramidase 2 (GBA2), by mutagenesis followed by kinetic characterization, X-ray crystallography, and ONIOM calculations on Thermoanaerobacterium xylanolyticum TxGH116, the structural model for GH116 enzymes. Mutations of residues that bind at the glucose C3OH and C4OH caused 27–196-fold increases in KM for p-nitrophenyl-β-D-glucoside, and significant decreases in the kcat, up to 5000-fold. At the C6OH binding residues, mutations of E777 decreased the kcat/KM by over 60,000-fold, while R786 mutants increased both the KM (40-fold) and kcat (2–4-fold). The crystal structures of R786A and R786K suggested a larger entrance to the active site could facilitate their faster rates. ONIOM binding energy calculations identified D452, H507, E777, and R786, along with the catalytic residues E441 and D593, as strong electrostatic contributors to glucose binding with predicted interaction energies > 15 kcal mol−1, consistent with the effects of the D452, H507, E777 and R786 mutations on enzyme kinetics. The relative importance of GH116 active site residues in substrate binding and catalysis identified in this work improves the prospects for the design of inhibitors for GBA2 and the engineering of GH116 enzymes for hydrolytic and synthetic applications. Full article
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