Applications of Structural Biology Techniques in Enzymology

A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Biological Processes and Systems".

Deadline for manuscript submissions: closed (5 September 2022) | Viewed by 8432

Special Issue Editor


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Guest Editor
Membrane Protein Crystallography Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
Interests: structural biology; biological chemistry; macromolecular crystallography; sulfur metabolism; hydrogen sulfide synthesis/breakdown; thiosulfate/tetrathionate interconversions; RNA processing; endoribonucleases; pathogenic bacteria

Special Issue Information

Dear Colleagues,

For several decades now, we have known that “structure is function”. Of course, we can invert this binomial relation and state that “function is structure”, i.e., each enzyme’s function is carefully regulated by a given fold or a specific set of three-dimensional arrays that tightly control each enzyme’s activity.

Enzymology in itself is a branch of biochemistry that aims to understand this relationship and provide insights into folding pathways, allosteric regulation, and catalytic mechanisms. However, enzymology calls upon a wide range of methods and disciplines providing answers to previously unanswered questions and conundrums. From molecular biology to molecular genetics, from biochemistry to biophysics, and from structural biology to biological chemistry, in no other field like in Enzymology can we gather so much knowledge on a given target regarding all these questions. Using a “from gene to structure” approach, enzymology and structural biology techniques are front-and-center disciplines in present-day science.

In this Special Issue, we will focus on “Applications of Structural Biology Techniques to Enzymology”. We aim to collect contributions covering a wide spectrum of disciplines and techniques providing an overview of the state-of-the-art methods and extensive repertoire of structural biology techniques that contribute to the field of enzymology.

Topics include but are not limited to:

  • Gene expression and protein production strategies;
  • Sample quality assessment for structural biology applications;
  • Biophysical characterization methodologies;
  • Biochemical characterization of enzymes and complexes;
  • Spectroscopic characterization of metalloenzymes (Mössbauer, Raman, XANES/EXAFS and EPR);
  • Structural biology techniques for three-dimensional structure determination (MX, NMR, SAXS and cryo-EM);
  • Enzyme function, specificity and catalysis;
  • Ways and means in Intrinsically Disorder Protein (ISPs) studies;
  • Structure-based enzyme technology for industrial, biomedical, biotechnological, and environmental applications;
  • Computational approaches to enzyme’s structure and function;
  • Integrative and disruptive methods in enzymology and/or structural biology.
Dr. José A. Brito
Guest Editor

Manuscript Submission Information

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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. Processes is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

  • enzymology
  • structural biology
  • biochemical and biophysical techniques
  • metalloenzyme spectroscopies
  • intrinsically disorder protein
  • structure–function relationship

Published Papers (2 papers)

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Research

14 pages, 2530 KiB  
Article
The Efficacy of Plant Enzymes Bromelain and Papain as a Tool for Reducing Gluten Immunogenicity from Wheat Bran
by Vijole Bradauskiene, Lina Vaiciulyte-Funk, Darius Cernauskas, Reda Dzingeleviciene, Joao P. M. Lima, Aida Bradauskaite and Mihaela Adriana Tita
Processes 2022, 10(10), 1948; https://doi.org/10.3390/pr10101948 - 27 Sep 2022
Cited by 4 | Viewed by 4906
Abstract
Gluten-free products made from naturally gluten-free raw materials have an inferior taste and can cause deficiencies in various nutrients, especially non-starch polysaccharides. To address this problem, scientists are searching for new strategies to eliminate harmful gluten from wheat, rye, and barley and to [...] Read more.
Gluten-free products made from naturally gluten-free raw materials have an inferior taste and can cause deficiencies in various nutrients, especially non-starch polysaccharides. To address this problem, scientists are searching for new strategies to eliminate harmful gluten from wheat, rye, and barley and to produce balanced products with good organoleptic properties. This study evaluated the possibility of hydrolysing gluten in wheat bran, a by-product obtained after the dry fractionation of wheat, using plant enzymes. The gluten content of wheat bran after treatment with papain, bromelain, and their combination under different hydrolysis conditions was investigated. The amount of gluten was determined using an enzyme-linked immunosorbent assay ELISA R5 and the reduction in immunogenic gliadins was analysed using high-performance reverse phase liquid chromatography. The results of the study showed that 4 h hydrolysis with bromelain and papain reduced the levels of gluten immunogenic compounds in bran from 58,650.00 to 2588.20–3544.50 mg/kg; however, they did not reach the gluten-free limit. A higher hydrolysis efficiency of 95.59% was observed after treatment with papain, while the combination of both enzymes and bromelain alone were less effective. The results presented in this article will be helpful to other researchers and manufacturers of wheat-based products when selecting methods to reduce gluten immunogenicity and contribute to the development of sustainable technologies. Full article
(This article belongs to the Special Issue Applications of Structural Biology Techniques in Enzymology)
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18 pages, 1894 KiB  
Article
High Throughput Expression Screening of Arabinofuranosyltransferases from Mycobacteria
by José Rodrigues, Vanessa T. Almeida, Ana L. Rosário, Yong Zi Tan, Brian Kloss, Filippo Mancia and Margarida Archer
Processes 2021, 9(4), 629; https://doi.org/10.3390/pr9040629 - 02 Apr 2021
Cited by 1 | Viewed by 2448
Abstract
Studies on membrane proteins can help to develop new drug targets and treatments for a variety of diseases. However, membrane proteins continue to be among the most challenging targets in structural biology. This uphill endeavor can be even harder for membrane proteins from [...] Read more.
Studies on membrane proteins can help to develop new drug targets and treatments for a variety of diseases. However, membrane proteins continue to be among the most challenging targets in structural biology. This uphill endeavor can be even harder for membrane proteins from Mycobacterium species, which are notoriously difficult to express in heterologous systems. Arabinofuranosyltransferases are involved in mycobacterial cell wall synthesis and thus potential targets for antituberculosis drugs. A set of 96 mycobacterial genes coding for Arabinofuranosyltransferases was selected, of which 17 were successfully expressed in E. coli and purified by metal-affinity chromatography. We herein present an efficient high-throughput strategy to screen in microplates a large number of targets from Mycobacteria and select the best conditions for large-scale protein production to pursue functional and structural studies. This methodology can be applied to other targets, is cost and time effective and can be implemented in common laboratories. Full article
(This article belongs to the Special Issue Applications of Structural Biology Techniques in Enzymology)
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