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Catalysts
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Catalysts for Structure-Functional Analysis and Enzyme Optimization
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Catalysts for Structure-Functional Analysis and Enzyme Optimization

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

Deadline for manuscript submissions: closed (10 January 2022) | Viewed by 5321

Special Issue Editors

Dr. Anna A. Kulminskaya

E-Mail Website
Guest Editor
Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Center “Kurchatov Institute”, Mkr. Orlova Roshcha, 1, 188300 Gatchina, Russia
Interests: screening for enzymatic activities; enzymology; enzyme engineering; transglycosylation; enzymatic synthesis of carbohydrates; glycoside–hydrolases
Dr. Vladimir V. Egorov

E-Mail Website
Guest Editor
Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute Named by B. P. Konstantinov of National Research Center “Kurchatov Institute”, 188300 Gatchina, Russia
Interests: protein folding, functional amyloids, conformational transitions, peptide inhibitors, antiviral drugs, supramolecular complexes

Special Issue Information

Dear Colleagues,

The knowledge of an enzyme’s catalytic mechanism can be of fundamental importance and a critical factor in the design and synthesis of compounds having biotechnological or therapeutic potential. The research is therefore multidisciplinary by its very nature and includes mechanistic enzymology, recombinant DNA (site-directed mutagenesis), as well as organic synthesis, medicinal/bioorganic chemistry, supramolecular chemistry, molecular modeling, and structural biology. Using the tools of chemo-organic synthesis, biochemistry, and computer modeling, this work aims to provide increased understanding of the chemical principles underlying mechanisms of action of natural catalysts with targeted activity. Structural models of the substrate enzyme complex are useful in order to investigate in detail the roles of the enzyme amino acid residues in its activity and the scope and limitation of substrates.

We invite researchers to contribute into this Special Issue in order to share their up-to-date knowledge on structure–functional aspects of enzyme functionality and achievements in engineering enzymes with new catalytic activity.

Dr. Anna A. Kulminskaya
Dr. Vladimir V. Egorov
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. Catalysts is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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
  • Protein engineering
  • Synthetic biology
  • Industrial enzymes
  • Bio-based chemicals
  • Enzyme structure
  • Protein folding
  • Peptide design
  • Supramolecular chemistry

Published Papers (2 papers)

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Research

15 pages, 10790 KiB  
Article
Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum
by Iuliia Iermak, Oksana Degtjarik, Petra Havlickova, Michal Kuty, Radka Chaloupkova, Jiri Damborsky, Tatyana Prudnikova and Ivana Kuta Smatanova
Catalysts 2021, 11(1), 5; https://0-doi-org.brum.beds.ac.uk/10.3390/catal11010005 - 23 Dec 2020
Cited by 1 | Viewed by 1974
Abstract
The activity of enzymes with active sites buried inside their protein core highly depends on the efficient transport of substrates and products between the active site and the bulk solvent. The engineering of access tunnels in order to increase or decrease catalytic activity [...] Read more.
The activity of enzymes with active sites buried inside their protein core highly depends on the efficient transport of substrates and products between the active site and the bulk solvent. The engineering of access tunnels in order to increase or decrease catalytic activity and specificity in a rational way is a challenging task. Here, we describe a combined experimental and computational approach to characterize the structural basis of altered activity in the haloalkane dehalogenase LinB D147C+L177C variant. While the overall protein fold is similar to the wild type enzyme and the other LinB variants, the access tunnels have been altered by introduced cysteines that were expected to form a disulfide bond. Surprisingly, the mutations have allowed several conformations of the amino acid chain in their vicinity, interfering with the structural analysis of the mutant by X-ray crystallography. The duration required for the growing of protein crystals changed from days to 1.5 years by introducing the substitutions. The haloalkane dehalogenase LinB D147C+L177C variant crystal structure was solved to 1.15 Å resolution, characterized and deposited to Protein Data Bank under PDB ID 6s06. Full article
(This article belongs to the Special Issue Catalysts for Structure-Functional Analysis and Enzyme Optimization)
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16 pages, 3293 KiB  
Article
Understanding the Effect of Multiple Domain Deletion in DNA Polymerase I from Geobacillus Sp. Strain SK72
by Waqiyuddin Hilmi Hadrawi, Anas Norazman, Fairolniza Mohd Shariff, Mohd Shukuri Mohamad Ali and Raja Noor Zaliha Raja Abd Rahman
Catalysts 2020, 10(8), 936; https://0-doi-org.brum.beds.ac.uk/10.3390/catal10080936 - 15 Aug 2020
Cited by 2 | Viewed by 2710
Abstract
The molecular structure of DNA polymerase I or family A polymerases is made up of three major domains that consist of a single polymerase domain with two extra exonuclease domains. When the N-terminal was deleted, the enzyme was still able to perform basic [...] Read more.
The molecular structure of DNA polymerase I or family A polymerases is made up of three major domains that consist of a single polymerase domain with two extra exonuclease domains. When the N-terminal was deleted, the enzyme was still able to perform basic polymerase activity with additional traits that used isothermal amplification. However, the 3′-5′ exonuclease domain that carries a proofreading activity was disabled. Yet, the structure remained attached to the 5′-3′ polymerization domain without affecting its ability. The purpose of this non-functional domain still remains scarce. It either gives negative effects or provides structural support to the DNA polymerase. Here, we compared the effect of deleting each domain against the polymerase activity. The recombinant wild type and its variants were successfully purified and characterized. Interestingly, SK72-Exo (a large fragment excluding the 5′-3′ exonuclease domain) exhibited better catalytic activity than the native SK72 (with all three domains) at similar optimum temperature and pH profile, and it showed longer stability at 70 °C. Meanwhile, SK72-Exo2 (polymerization domain without both the 5′-3′ and 3′-5′ exonuclease domain) displayed the lowest activity with an optimum at 40 °C and favored a more neutral environment. It was also the least stable among the variants, with almost no activity at 50 °C for the first 10 min. In conclusion, cutting both exonuclease domains in DNA polymerase I has a detrimental effect on the polymerization activity and structural stability. Full article
(This article belongs to the Special Issue Catalysts for Structure-Functional Analysis and Enzyme Optimization)
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