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Advanced Research on Enzymes in Biocatalysis
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Advanced Research on Enzymes in Biocatalysis

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: 20 February 2026 | Viewed by 1403

Special Issue Editors

Dr. Simona Varriale

E-Mail Website
Guest Editor
Department of Chemical Sciences, University Federico II of Naples, Via Cinthia, 4, 80126 Naples, Italy
Interests: biorefinery; biomass valorisation; deep eutectic solvents; enzyme improvement; molecular docking
Dr. Samuel De Visser

E-Mail Website
Guest Editor
Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
Interests: computational chemistry; density functional theory; QM/MM; reaction mechanisms; biomimetic models; enzyme catalysis
Special Issues, Collections and Topics in MDPI journals
Dr. Salvatore Fusco

E-Mail Website
Guest Editor
Department of Biotechnology, University of Verona, 37134 Verona, Italy
Interests: industrial enzymology; extremozymes; biocatalysis; biorefinery; biomass valorisation; enzymatic recycling of plastics; protein engineering; CRISPR-based applications; virus biotechnology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biocatalysis represents a key technology for sustainable and efficient chemical processes, leveraging the remarkable specificity and catalytic power of enzymes. From industrial bioprocesses to novel biorefinery strategies, enzyme-based approaches are transforming sectors such as pharmaceuticals, food, biofuels, and materials science.

This Special Issue aims to highlight cutting-edge advancements in enzyme engineering, bioprocess development, and computational strategies to optimize biocatalytic systems. We welcome contributions on enzyme discovery, immobilization techniques, cascade biocatalysis, and innovative bioprocessing approaches. Topics of interest include molecular and computational design of enzymes, machine learning-assisted enzyme engineering, and applications of enzymatic catalysis in green chemistry and biomass valorisation.

By bringing together experimental and theoretical insights, this issue will provide a comprehensive view of current trends and future directions in biocatalysis. Researchers in academia and industry are invited to contribute original research articles, reviews, and short communications.

Dr. Simona Varriale
Dr. Samuel De Visser
Dr. Salvatore Fusco
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biocatalysis
  • bioprocess
  • enzyme immobilization
  • enzyme production
  • response surface methodology (RSM)
  • enzymatic-assisted extraction
  • enzymatic-catalyzed synthesis
  • enzyme modelling
  • bioreactor
  • bioconversion
  • cascade biocatalysis
  • enzymatic kinetic
  • enzyme engineering
  • ultrasound-assisted enzymatic reaction
  • directed evolution
  • machine learning-assisted enzyme engineering
  • waste-to-value bioprocesses

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Published Papers (3 papers)

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Research

18 pages, 3956 KB  
Article
Substrate Specificity and Peptide Motif Preferences of β-Lytic and L5 Proteases from Lysobacter spp. Revealed by LC–MS/MS Analysis
by Mihail Konstantinov, Leonid Kaluzhskiy, Evgeniy Yablokov, Dmitry Zhdanov, Alexis Ivanov and Ilya Toropygin
Int. J. Mol. Sci. 2025, 26(17), 8603; https://doi.org/10.3390/ijms26178603 - 4 Sep 2025
Viewed by 121
Abstract
β-Lytic protease (Blp) and protease L5 are enzymes from Lysobacter bacteria with distinct proteolytic and bacteriolytic activities. To characterize their substrate specificity, we employed liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis following hydrolysis of fractionated protein mixtures. Heatmaps and sequence logos revealed a pronounced [...] Read more.
β-Lytic protease (Blp) and protease L5 are enzymes from Lysobacter bacteria with distinct proteolytic and bacteriolytic activities. To characterize their substrate specificity, we employed liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis following hydrolysis of fractionated protein mixtures. Heatmaps and sequence logos revealed a pronounced specificity of Blp towards glycine and lysine residues, while L5 preferentially cleaved non-polar residues such as methionine, phenylalanine, and leucine. Notably, proline was frequently observed at the P2 position in L5 substrates. Comparative analysis with trypsin revealed that L5 generated significantly shorter peptides, whereas Blp produced fragments similar in length to tryptic peptides. These findings indicate different cleavage preferences and suggest potential applications for these enzymes in proteomic analysis. Full article
(This article belongs to the Special Issue Advanced Research on Enzymes in Biocatalysis)
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18 pages, 2057 KB  
Article
Contribution of Second-Shell Residues to PLP-Dependent Transaminase Catalysis: A Case Study of D-Amino Acid Transaminase from Desulfomonile tiedjei
by Alina K. Bakunova, Iuliia V. Rudina, Vladimir O. Popov and Ekaterina Yu. Bezsudnova
Int. J. Mol. Sci. 2025, 26(17), 8536; https://doi.org/10.3390/ijms26178536 - 2 Sep 2025
Viewed by 287
Abstract
Understanding the structure–function relationships of pyridoxal-5′-phosphate (PLP)-dependent transaminases is key to advancing pyridoxal-phosphate-dependent catalysis and engineering transaminases for industrial applications. Despite our extensive knowledge of PLP-dependent enzymatic reactions, engineering transaminase activity and stability remains challenging. Here, we present the functional characterization of a [...] Read more.
Understanding the structure–function relationships of pyridoxal-5′-phosphate (PLP)-dependent transaminases is key to advancing pyridoxal-phosphate-dependent catalysis and engineering transaminases for industrial applications. Despite our extensive knowledge of PLP-dependent enzymatic reactions, engineering transaminase activity and stability remains challenging. Here, we present the functional characterization of a novel PLP-dependent fold type IV transaminase from Desulfomonile tiedjei, alongside a detailed analysis of PLP binding and holoenzyme stability. This new transaminase exhibits activity toward various D-amino acids and (R)-phenylethylamine. Structural modeling and site-directed mutagenesis of residues in the second shell of the PLP-binding site revealed their roles in cofactor binding and the transaminase’s catalytic efficiency. Notably, the T199Q variant demonstrated a fivefold increase in PLP affinity and improved activity under alkaline conditions. This is attributed to a newly formed hydrogen bond that stabilizes the N1-binding region of PLP. Glutamine at position 199 is not observed in homologous transaminases, making this non-natural substitution a novel and beneficial modification. These findings emphasize the importance of second-shell interactions in stabilizing PLP and expand our understanding of the structural diversity within PLP fold type IV transaminases. This paves the way for the engineering of more stable and versatile biocatalysts for industrial applications. Full article
(This article belongs to the Special Issue Advanced Research on Enzymes in Biocatalysis)
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13 pages, 2812 KB  
Article
Fungal Laccases with High and Medium Redox Potential: Is the T1 Center Potential a Key Characteristic of Catalytic Efficiency in Heterogeneous and Homogeneous Reactions?
by Olga Morozova, Maria Khlupova, Irina Vasil’eva, Alexander Yaropolov and Tatyana Fedorova
Int. J. Mol. Sci. 2025, 26(15), 7488; https://doi.org/10.3390/ijms26157488 - 2 Aug 2025
Viewed by 386
Abstract
Catalytic and bioelectrocatalytic properties of four white rot fungal laccases (Trametes hirsuta, ThL; Coriolopsis caperata, CcL; Steccherinum murashkinskyi, SmL; and Antrodiella faginea, AfL) from different orthologous groups were comparatively studied in homogeneous reactions of electron donor substrate oxidation [...] Read more.
Catalytic and bioelectrocatalytic properties of four white rot fungal laccases (Trametes hirsuta, ThL; Coriolopsis caperata, CcL; Steccherinum murashkinskyi, SmL; and Antrodiella faginea, AfL) from different orthologous groups were comparatively studied in homogeneous reactions of electron donor substrate oxidation and in a heterogeneous reaction of dioxygen electroreduction. The ThL and CcL laccases belong to high-redox-potential enzymes (E0T1 = 780 mV), while the AfL and SmL laccases are medium-redox-potential enzymes (E0T1 = 620 and 650 mV). We evaluated the efficiency of laccases in mediatorless bioelectrocatalytic dioxygen reduction by the steady-state potential (Ess), onset potential (Eonset), half-wave potential (E1/2), and the slope of the linear segment of the polarization curve. A good correlation was observed between the T1 center potential of the laccases and their electrocatalytic characteristics; however, no correlation with the homogeneous reactions of electron donor substrates’ oxidation was detected. The results obtained are discussed in the light of the known data on the three-dimensional structures of the laccases studied. Full article
(This article belongs to the Special Issue Advanced Research on Enzymes in Biocatalysis)
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