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Symmetry
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Symmetry and Its Application in the Structural and Biochemical Characterization...
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Symmetry and Its Application in the Structural and Biochemical Characterization of Enzymes and Protein Complexes

A special issue of Symmetry (ISSN 2073-8994). This special issue belongs to the section "Life Sciences".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 9250

Special Issue Editor

Dr. Oleg A. Zadvornyy

E-Mail Website
Guest Editor
Chemistry and Biochemistry Department, Montana State University, 103 Chemistry and Biochemistry Building, Bozeman, MT 59715, USA
Interests: structural biology; biochemistry

Special Issue Information

Dear Colleagues,

This Special Issue will be dedicated to understanding the significance of symmetry in biological systems, enzymes and protein complexes. We invite you to participate in this Special Issue and submit experimental and theoretical research, reviews and short communication papers that discuss the importance of symmetry in protein structure–function relationships: 1) the importance of symmetry for protein tertiary and quaternary structures and how it influences protein folding, function, evolution and stability; 2) how the symmetry of biological molecules can change in response to biological and chemical stimuli; 3) the ability of protein subunits to form large symmetrical or asymmetrical protein complexes such as viral capsids or filament-like structures; 4) symmetric or asymmetric cooperative motions in homo-oligomeric protein complexes and their importance in changes at the active site and in ligand binding or release; 5) the role of symmetry in stereoselective substrate recognition; and 6) the development of software for the detection of internal symmetry in protein complexes.

Dr. Oleg A. Zadvornyy
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. Symmetry 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 2400 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

  • symmetry of protein complexes
  • protein assembly and dynamics
  • protein interactions
  • quaternary structure
  • groups and topology of quaternary structures
  • quaternary structure evolution
  • homomer
  • heteromer
  • oligomer
  • multimer
  • self-assembly
  • peptide assembly
  • peptide geometry and symmetry groups
  • ɑ-helix
  • coiled coil packing and geometry
  • computed structure models

Published Papers (3 papers)

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Research

14 pages, 4396 KiB  
Article
Oligomeric Symmetry of Purine Nucleoside Phosphorylases
by Boris Gomaz and Zoran Štefanić
Symmetry 2024, 16(1), 124; https://0-doi-org.brum.beds.ac.uk/10.3390/sym16010124 - 19 Jan 2024
Viewed by 747
Abstract
Many enzymes are composed of several identical subunits, which are arranged in a regular fashion and usually comply with some definite symmetry. This symmetry may be approximate or exact and may or may not coincide with the symmetry of crystallographic packing. Purine nucleoside [...] Read more.
Many enzymes are composed of several identical subunits, which are arranged in a regular fashion and usually comply with some definite symmetry. This symmetry may be approximate or exact and may or may not coincide with the symmetry of crystallographic packing. Purine nucleoside phosphorylases (PNP) are a class of oligomeric enzymes that show an interesting interplay between their internal symmetry and the symmetry of their crystal packings. There are two main classes of this enzyme: trimeric PNPs, or “low-molecular-mass” proteins, which are found mostly in eukaryotic organisms, and hexameric PNPs, or “high-molecular-mass” proteins, which are found mostly in prokaryotic organisms. Interestingly, these two enzyme classes share only 20–30% sequence identity, but the overall fold of the single monomer is similar, yet this monomeric building block results in a different quaternary structure. To investigate this interplay of symmetry in this class of enzymes, a comprehensive database of all PNPs is constructed, containing their local symmetries and interface information. Full article
(This article belongs to the Special Issue Symmetry and Its Application in the Structural and Biochemical Characterization of Enzymes and Protein Complexes)
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9 pages, 1690 KiB  
Communication
Structural and Biochemical Basis of Etoposide-Resistant Mutations in Topoisomerase IIα
by Elizabeth G. Gibson and Joseph E. Deweese
Symmetry 2022, 14(7), 1309; https://0-doi-org.brum.beds.ac.uk/10.3390/sym14071309 - 24 Jun 2022
Cited by 2 | Viewed by 1593
Abstract
Etoposide is a widely used anticancer drug that targets type II topoisomerases, including topoisomerase IIα (TOP2A). TOP2A is a nuclear enzyme involved in regulating DNA topology through a double-strand passage mechanism. TOP2A is a homodimeric enzyme with two symmetrical active sites formed by [...] Read more.
Etoposide is a widely used anticancer drug that targets type II topoisomerases, including topoisomerase IIα (TOP2A). TOP2A is a nuclear enzyme involved in regulating DNA topology through a double-strand passage mechanism. TOP2A is a homodimeric enzyme with two symmetrical active sites formed by residues from either half of the dimer. Both active sites cleave DNA, forming an enzyme-bound, double-stranded DNA break. Etoposide acts by binding in the active site between the ends of cleaved DNA, preventing the enzyme from ligating the DNA. In the present study, biochemical and structural data are used to examine the mechanism of etoposide resistance found with specific point mutations in TOP2A. Mutations near the active site (D463A, G534R, R487K), along with some outside of the active site (ΔA429 and P716L), are examined. We hypothesize that changes in the coordination of DNA cleavage results from mutations that impact symmetrical relationships in the active site and surrounding regions. In some cases, we report the first data on purified versions of these enzymes. Based upon our results, both local and long-distance factors can impact etoposide action and may indicate interdependent relationships in structure and function. Full article
(This article belongs to the Special Issue Symmetry and Its Application in the Structural and Biochemical Characterization of Enzymes and Protein Complexes)
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15 pages, 2837 KiB  
Article
In Silico Investigation on the Interaction of Chiral Phytochemicals from Opuntia ficus-indica with SARS-CoV-2 Mpro
by Caterina Vicidomini, Valentina Roviello and Giovanni N. Roviello
Symmetry 2021, 13(6), 1041; https://0-doi-org.brum.beds.ac.uk/10.3390/sym13061041 - 09 Jun 2021
Cited by 35 | Viewed by 5456
Abstract
Opuntia ficus-indica is a cactaceous plant native to America but, nowadays, widely found worldwide, having been the most common domesticated species of cactus grown as a crop plant in semiarid and arid parts of the globe, including several Mediterranean basin countries. Opuntia ficus-indica [...] Read more.
Opuntia ficus-indica is a cactaceous plant native to America but, nowadays, widely found worldwide, having been the most common domesticated species of cactus grown as a crop plant in semiarid and arid parts of the globe, including several Mediterranean basin countries. Opuntia ficus-indica can be regarded as a medicinal plant, being source of numerous bioactive phytochemicals such as vitamins, polyphenols, and amino acids. The urgent need for therapeutic treatments for the COronaVIrus Disease 19 (COVID-19), caused by the Severe Acute Respiratory Syndrome (SARS)-Coronavirus (CoV)-2, justifies the great attention currently being paid not only to repurposed antiviral drugs, but also to natural products and herbal medications. In this context, the anti-COVID-19 utility of Opuntia ficus-indica as source of potential antiviral drugs was investigated in this work on the basis of the activity of some of its phytochemical constituents. The antiviral potential was evaluated in silico in docking experiments with Mpro, i.e., the main protease of SARS-CoV-2, that is one of the most investigated protein targets of therapeutic strategies for COVID-19. By using two web-based molecular docking programs (1-Click Mcule and COVID-19 Docking Server), we found, for several flavonols and flavonol glucosides isolated from Opuntia ficus-indica, good binding affinities for Mpro, and in particular, binding energies lower than −7.0 kcal/mol were predicted for astragalin, isorhamnetin, isorhamnetin 3-O-glucoside, 3-O-caffeoyl quinic acid, and quercetin 5,4′-dimethyl ether. Among these compounds, the chiral compound astragalin showed in our in silico studies the highest affinity for Mpro (−8.7 kcal/mol) and also a low toxicity profile, emerging, thus, as an interesting protease inhibitor candidate for anti-COVID-19 strategies. Full article
(This article belongs to the Special Issue Symmetry and Its Application in the Structural and Biochemical Characterization of Enzymes and Protein Complexes)
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