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Symmetry
Special Issues
Symmetry in Structural Biology and Protein Characterization
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Symmetry in Structural Biology and Protein Characterization

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

Deadline for manuscript submissions: closed (19 February 2023) | Viewed by 2250

Special Issue Editors

Dr. Eustace Y. Fernando

E-Mail Website1 Website2
Guest Editor
Department of Biological Sciences, Faculty of Applied Sciences, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka
Interests: bio-electrochemical systems (BES); microbial ecology and interactions; microbial biotechnology; renewable microbial bioenergy/biofuels; microbial biopolymers; molecular and single-cell microbiology and proteomics
Dr. Henrik Bech Kjeldal

E-Mail Website
Co-Guest Editor
Section of Biotechnology, Fredrik Bajers Vej 7, H, 1-539, 9220 Aalborg, Denmark
Interests: mass spectrometry; bioinformatics; biochemistry; proteins; shotgun Proteomics; MALDI-TOF MS; protein purification; protein identification; isotope labeling; quantitative spectrometry
Dr. Marc Rhyan Anthony Puno

E-Mail Website
Co-Guest Editor
Memorial Sloan Kettering Cancer Center, Box 399 1275 York Avenue, New York, NY 10065, USA
Interests: protein structure; X-Ray crystallography; recombinant DNA technology

Special Issue Information

Dear Colleagues,

Modern structural biology and protein characterization draws from many disciplines, such as crystallography, X-ray diffraction, cryo-electron microscopy, protein purification and biochemistry. The symmetric nature of many biological macromolecules and macromolecular assemblies such as the tertiary and quaternary structures of proteins and enzymes often carries functional significance, such as being a vital feature in inducing and sustaining catalysis. This Special Issue examines the symmetric nature of biological macromolecular assemblies, the contribution of their structural traits to maintaining proper biological function and different hierarchical levels of biostructural organization. It also welcomes original research articles, short communications and review papers on the molecular characterization and structural assembly features of polypeptides, globular proteins, protein quaternary structure, viruses, nucleic acids, tubular crystals and ordinary three-dimensional crystal assemblies of biological macromolecules. Studies using novel technical developments such as cryo-electron microscopy in deducing the structure of biological macromolecular assemblies are also welcome to be submitted for publication in this Special Issue.

Dr. Eustace Y. Fernando
Guest Editor

Dr. Henrik Bech Kjeldal
Dr. Marc Rhyan Anthony Puno
Co-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. 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

  • biological macromolecules
  • structural biology
  • protein characterization
  • cryo-electron microscopy
  • X-ray crystallography
  • nuclear magnetic resonance (NMR) studies of macromolecules
  • symmetry in macromolecular assembly
  • symmetry in catalysis

Published Papers (1 paper)

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Research

20 pages, 5955 KiB  
Article
Exploration of the Structural Asymmetry Induced by the Intrinsic Flexibility of HIV-2 Protease
by Anne Badel, Laëtitia Breuil, Pierre Laville and Leslie Regad
Symmetry 2022, 14(2), 362; https://doi.org/10.3390/sym14020362 - 11 Feb 2022
Viewed by 1507
Abstract
HIV-2 protease (PR2) is a homodimer targeted by drugs in the treatment of HIV-2 infections. This dimer is often considered symmetric. However, exploration of crystallographic structures showed that the two chains of PR2 exhibit different conformations. This study presents the first analysis of [...] Read more.
HIV-2 protease (PR2) is a homodimer targeted by drugs in the treatment of HIV-2 infections. This dimer is often considered symmetric. However, exploration of crystallographic structures showed that the two chains of PR2 exhibit different conformations. This study presents the first analysis of the structural asymmetry of PR2 induced by its intrinsic flexibility. We followed the structural asymmetry of PR2 throughout a molecular dynamics (MD) simulation of 1 microsecond. To do so, we quantified the global and local structural asymmetries of 1001 structures extracted from the MD simulation using the root mean square deviation (RMSD) between the two chains in each structure. We then analyzed the links between global and local asymmetry and PR2 flexibility. Our results showed that the global asymmetry of PR2 evolves over time and that it is not explained by the asymmetry of only one region of PR2. We noted that the most flexible regions of PR2 are the most asymmetric regions, revealing that the structural asymmetry of a region is induced by its intrinsic flexibility. Using multivariate analysis methods, we identified six asymmetric profiles varying from structures exhibiting weak asymmetry to structures with extreme asymmetry in at least eight different regions. The analysis of transitions between the different profiles in the MD simulation showed that two consecutive structures often exhibit similar asymmetric profiles, revealing small deformations. To conclude, this study provides insights which help to better understand PR2’s structure, dynamics, and deformations. Full article
(This article belongs to the Special Issue Symmetry in Structural Biology and Protein Characterization)
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