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Design of Biocatalysts and Their Applications for Asymmetric Transformations, C-C Bond Formation and Biodegradation

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

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 3899

Special Issue Editor

Dr. Ekaterina Yu. Bezsudnova

E-Mail Website
Guest Editor
Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia
Interests: enzymology; structure-function relationships in proteins; thermostability of enzymes; enzyme stability in water-organic solvent media; transaminases; dehydrogenases; biocatalysis

Special Issue Information

Dear Colleagues,

A huge diversity of natural enzymes and accessibility of metagenomic and metabolomic data together with progress in protein engineering tools created a powerful platform for the development of biocatalysts for chemical transformations. Incorporation of single-step enzymatic transformation into the chemical process, development of chemoenzymatic processes or multi-step enzymatic cascades became available due to high-level expression of enzymes, effective approaches for stabilization of enzymes, modification of enzyme’s substrate scope and in-depth understanding of natural synthetic processes.

Great progress is observed in enzyme applications for the synthesis of non-natural compounds and the construction of artificial enzymes. These achievements are based on fundamental knowledge of structure-function relationships in enzymes and a deep understanding of active site architecture. Despite high throughput methods for the design of enzymes and enzymatic cascades, the development of a stable effective biocatalyst is still a time-consuming task, that requires knowledge and skills in various fields of biochemistry, molecular biology, and organic chemistry.

With this Special Issue, we aim to collect original research articles, review articles, and short communications dealing with the development of biocatalysts (both discovery of new enzymes and the design of enzymes for the process). Fundamental studies on the molecular basis of the stability of enzymes in harsh industrial environments, including water-organic solvent media are welcome. 

Suitable topics include, but are not limited to:

  • Development of biocatalysts by rational design, directed evolution, in silico approaches, etc
  • Change in substrate scope, tuning of enzyme’s active site for productive binding of complex substrates
  • Enhancement of enzyme’s stability, stereoselectivity and turnover
  • Fundamental studies on the enzyme’s stability in water-organic solvent media
  • Biocatalysts with non-canonical amino acids
  • Industrial enzymes discovered using metagenomic libraries (metagenomic screening approaches)
  • Development of biocatalysts for asymmetric transformations, functionalization reactions, including C-H bond oxidation.
  • Biocatalytic cascade development
  • Application of enzymes in chemoenzymatic synthesis
  • Application of enzymes in C-C bond formation and breaking.
  • Elaboration of novel enzymatic mechanisms
  • Non-natural products biosynthesis
  • Artificial biocatalytic cascade reactions
  • Photo-biocatalysis
  • Enzymatic recycling of plastics

Dr. Ekaterina Yu. Bezsudnova
Guest Editor

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

  • biocatalyst
  • stability of enzymes
  • non-natural products
  • cascade reactions
  • substrate scope
  • photo-biocatalysis
  • applications of enzymes
  • biocatalysis

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Published Papers (3 papers)

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Research

17 pages, 2306 KiB  
Article
Catalytic Stability of S-1-(4-Hydroxyphenyl)-Ethanol Dehydrogenase from Aromatoleum aromaticum
by Mateusz Tataruch, Viera Illeová, Anna Kluza, Patrik Cabadaj and Milan Polakovič
Int. J. Mol. Sci. 2024, 25(13), 7385; https://doi.org/10.3390/ijms25137385 - 5 Jul 2024
Viewed by 564
Abstract
Derived from the denitrifying bacterium Aromatoleum aromaticum EbN1 (Azoarcus sp.), the enzyme S-1-(4-hydroxyphenyl)-ethanol dehydrogenase (S-HPED) belongs to the short-chain dehydrogenase/reductase family. Using research techniques like UV-Vis spectroscopy, dynamic light scattering, thermal-shift assay and HPLC, we investigated the catalytic and structural stability [...] Read more.
Derived from the denitrifying bacterium Aromatoleum aromaticum EbN1 (Azoarcus sp.), the enzyme S-1-(4-hydroxyphenyl)-ethanol dehydrogenase (S-HPED) belongs to the short-chain dehydrogenase/reductase family. Using research techniques like UV-Vis spectroscopy, dynamic light scattering, thermal-shift assay and HPLC, we investigated the catalytic and structural stability of S-HPED over a wide temperature range and within the pH range of 5.5 to 9.0 under storage and reaction conditions. The relationship between aggregation and inactivation of the enzyme in various pH environments was also examined and interpreted. At pH 9.0, where the enzyme exhibited no aggregation, we characterized thermally induced enzyme inactivation. Through isothermal and multitemperature analysis of inactivation data, we identified and confirmed the first-order inactivation mechanism under these pH conditions and determined the kinetic parameters of the inactivation process. Additionally, we report the positive impact of glucose as an enzyme stabilizer, which slows down the dynamics of S-HPED inactivation over a wide range of pH and temperature and limits enzyme aggregation. Besides characterizing the stability of S-HPED, the enzyme’s catalytic activity and high stereospecificity for 10 prochiral carbonyl compounds were positively verified, thus expanding the spectrum of substrates reduced by S-HPED. Our research contributes to advancing knowledge about the biocatalytic potential of this catalyst. Full article
(This article belongs to the Special Issue Design of Biocatalysts and Their Applications for Asymmetric Transformations, C-C Bond Formation and Biodegradation)
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16 pages, 3748 KiB  
Article
Expanded Substrate Specificity in D-Amino Acid Transaminases: A Case Study of Transaminase from Blastococcus saxobsidens
by Sofia A. Shilova, Ilya O. Matyuta, Elizaveta S. Petrova, Alena Y. Nikolaeva, Tatiana V. Rakitina, Mikhail E. Minyaev, Konstantin M. Boyko, Vladimir O. Popov and Ekaterina Yu. Bezsudnova
Int. J. Mol. Sci. 2023, 24(22), 16194; https://doi.org/10.3390/ijms242216194 - 10 Nov 2023
Cited by 1 | Viewed by 1279
Abstract
Enzymes with expanded substrate specificity are good starting points for the design of biocatalysts for target reactions. However, the structural basis of the expanded substrate specificity is still elusive, especially in the superfamily of pyridoxal-5′-phosphate-dependent transaminases, which are characterized by a conserved organization [...] Read more.
Enzymes with expanded substrate specificity are good starting points for the design of biocatalysts for target reactions. However, the structural basis of the expanded substrate specificity is still elusive, especially in the superfamily of pyridoxal-5′-phosphate-dependent transaminases, which are characterized by a conserved organization of both the active site and functional dimer. Here, we analyze the structure–function relationships in a non-canonical D-amino acid transaminase from Blastococcus saxobsidens, which is active towards D-amino acids and primary (R)-amines. A detailed study of the enzyme includes a kinetic analysis of its substrate scope and a structural analysis of the holoenzyme and its complex with phenylhydrazine—a reversible inhibitor and analogue of (R)-1-phenylethylamine—a benchmark substrate of (R)-selective amine transaminases. We suggest that the features of the active site of transaminase from B. saxobsidens, such as the flexibility of the R34 and R96 residues, the lack of bulky residues in the β-turn at the entrance to the active site, and the short O-pocket loop, facilitate the binding of substrates with and without α-carboxylate groups. The proposed structural determinants of the expanded substrate specificity can be used for the design of transaminases for the stereoselective amination of keto compounds. Full article
(This article belongs to the Special Issue Design of Biocatalysts and Their Applications for Asymmetric Transformations, C-C Bond Formation and Biodegradation)
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21 pages, 1837 KiB  
Article
Biodiesel Production Using Palm Oil with a MOF-Lipase B Biocatalyst from Candida Antarctica: A Kinetic and Thermodynamic Study
by Liliana Giraldo, Fernando Gómez-Granados and Juan Carlos Moreno-Piraján
Int. J. Mol. Sci. 2023, 24(13), 10741; https://doi.org/10.3390/ijms241310741 - 28 Jun 2023
Cited by 5 | Viewed by 1621
Abstract
This research presents the results of the immobilization of Candida Antarctica Lipase B (CALB) on MOF-199 and ZIF-8 and its use in the production of biodiesel through the transesterification reaction using African Palm Oil (APO). The results show that the highest adsorption capacity, [...] Read more.
This research presents the results of the immobilization of Candida Antarctica Lipase B (CALB) on MOF-199 and ZIF-8 and its use in the production of biodiesel through the transesterification reaction using African Palm Oil (APO). The results show that the highest adsorption capacity, the 26.9 mg·g−1 Lipase, was achieved using ZIF-8 at 45 °C and an initial protein concentration of 1.20 mg·mL−1. The results obtained for the adsorption equilibrium studies allow us to infer that CALB was physically adsorbed on ZIF-8 while chemically adsorbed with MOF-199. It was determined that the adsorption between Lipase and the MOFs under study better fit the Sips isotherm model. The results of the kinetic studies show that adsorption kinetics follow the Elovich model for the two synthesized biocatalysts. This research shows that under the experimental conditions in which the studies were carried out, the adsorption processes are a function of the intraparticle and film diffusion models. According to the results, the prepared biocatalysts showed a high efficiency in the transesterification reaction to produce biodiesel, with methanol as a co-solvent medium. In this work, the catalytic studies for the imidazolate, ZIF-8, presented more catalytic activity when used with CALB. This system presented 95% biodiesel conversion, while the biocatalyst formed by MOF-199 and CALB generated a catalytic conversion percentage of 90%. Although both percentages are high, it should be noted that CALB-MOF-199 presented better reusability, which is due to chemical interactions. Full article
(This article belongs to the Special Issue Design of Biocatalysts and Their Applications for Asymmetric Transformations, C-C Bond Formation and Biodegradation)
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