Symmetry in Molecular Biology

A special issue of Symmetry (ISSN 2073-8994). This special issue belongs to the section "Chemistry: Symmetry/Asymmetry".

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 33369

Special Issue Editors


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Guest Editor
Division of Physical Chemistry, Institute Ruder Boskovic, Zagreb, Croatia

E-Mail Website
Guest Editor
Division of Physical Chemistry, Institute Ruder Boskovic, Zagreb, Croatia

Special Issue Information

Dear Colleagues,

Symmetry is one of the ubiquitous concepts in science, impacting very diverse phenomena, such as the very beginning of the Universe all the way through to the appearance of life on Earth, the laws of its evolution and the ever-inspiring wonders of the molecular machinery of living beings. It sets the stage for everything in the physical world as physics seeks and, with much success, manages to unify all the fundamental forces in super-symmetrical grand unification. This stage is filled with a multitude of players that whirl on it in a myriad of fascinating ways that make up the multiple organizational levels of living cells. The interplay of symmetry and asymmetry seems to be built into life itself, and it appears on all structural levels: From symmetric spherical atoms that join into chiral amino acids, which then join to make asymmetric protein chains that often join into more complex and symmetrical oligomers, which then join into fascinating symmetrical viruses. The timescale of their interconversions can be entirely different, and it might be one of the reasons for controversial comments and conclusions. There is no logical requirement for a preference for any of these two organizations of a living body, and they are the result of evolutionary or developmental adaptation. Symmetry breaking is necessary in many living processes, such as proper orientation of the mitotic spindle in asymmetrical cell division, as a key mechanism in cell differentiation, unidirectional transport through membranes, asymmetric organogenesis (gut, heart and brain), and so on. Newly developed mathematical models allow the elucidation of universal principles in cell polarity studying organization and transport through membranes and shed light on 'dualism' in the life cycle of a living cell.

This Special Issue will be devoted to all aspects of symmetry in the domain of molecular biology. The topics covered will be the following but not limited to:

  • Symmetry and asymmetry in structural and functional cellular organization of biomacromolecules;
  • Art of biovisualization;
  • Symmetry towards asymmetry of life molecules in relation to their biological functions—homochirality of basic constituents;
  • Symmetry of viruses

Dr. Biserka Kojic Prodic
Dr. Zoran Štefanić
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.

Published Papers (3 papers)

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Research

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22 pages, 784 KiB  
Article
Icosadeltahedral Geometry of Geodesic Domes, Fullerenes and Viruses: A Tutorial on the T-Number
by Antonio Šiber
Symmetry 2020, 12(4), 556; https://doi.org/10.3390/sym12040556 - 04 Apr 2020
Cited by 12 | Viewed by 13856
Abstract
The Caspar–Klug (CK) classification of viruses is discussed by parallel examination of geometry of icosahedral geodesic domes, fullerenes, and viruses. The underlying symmetry of all structures is explained and thoroughly visually represented. Euler’s theorem on polyhedra is used to calculate the number of [...] Read more.
The Caspar–Klug (CK) classification of viruses is discussed by parallel examination of geometry of icosahedral geodesic domes, fullerenes, and viruses. The underlying symmetry of all structures is explained and thoroughly visually represented. Euler’s theorem on polyhedra is used to calculate the number of vertices, edges, and faces in domes, number of atoms, bonds, and pentagonal and hexagonal rings in fullerenes, and number of proteins and protein–protein contacts in viruses. The T-number, the characteristic for the CK classification, is defined and discussed. The superposition of fullerene and dome designs is used to obtain a representation of a CK virus with all the proteins indicated. Some modifications of the CK classifications are sketched, including elongation of the CK blueprint, fusion of two CK blueprints, dodecahedral view of the CK shapes, and generalized CK designs without a clearly visible geometry of the icosahedron. These are compared to cases of existing viruses. Full article
(This article belongs to the Special Issue Symmetry in Molecular Biology)
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11 pages, 5509 KiB  
Article
Symmetry at the Cellular Mesoscale
by David S. Goodsell
Symmetry 2019, 11(9), 1170; https://doi.org/10.3390/sym11091170 - 16 Sep 2019
Cited by 4 | Viewed by 5595
Abstract
Symmetry plays a functional role in the structure and action of biomolecules and their associations and interactions in living cells. This symmetry is a natural consequence of the evolutionary mechanisms that lead to the development of life, and it ranges from perfect point-group [...] Read more.
Symmetry plays a functional role in the structure and action of biomolecules and their associations and interactions in living cells. This symmetry is a natural consequence of the evolutionary mechanisms that lead to the development of life, and it ranges from perfect point-group symmetry in protein oligomers to more approximate symmetries in the higher-order mesoscale structure of cellular environments. Full article
(This article belongs to the Special Issue Symmetry in Molecular Biology)
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Review

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18 pages, 4031 KiB  
Review
Symmetry in Nucleic-Acid Double Helices
by Udo Heinemann and Yvette Roske
Symmetry 2020, 12(5), 737; https://doi.org/10.3390/sym12050737 - 05 May 2020
Cited by 15 | Viewed by 12893
Abstract
In nature and in the test tube, nucleic acids occur in many different forms. Apart from single-stranded, coiled molecules, DNA and RNA prefer to form helical arrangements, in which the bases are stacked to shield their hydrophobic surfaces and expose their polar edges. [...] Read more.
In nature and in the test tube, nucleic acids occur in many different forms. Apart from single-stranded, coiled molecules, DNA and RNA prefer to form helical arrangements, in which the bases are stacked to shield their hydrophobic surfaces and expose their polar edges. Focusing on double helices, we describe the crucial role played by symmetry in shaping DNA and RNA structure. The base pairs in nucleic-acid double helices display rotational pseudo-symmetry. In the Watson–Crick base pairs found in naturally occurring DNA and RNA duplexes, the symmetry axis lies in the base-pair plane, giving rise to two different helical grooves. In contrast, anti-Watson–Crick base pairs have a dyad axis perpendicular to the base-pair plane and identical grooves. In combination with the base-pair symmetry, the syn/anti conformation of paired nucleotides determines the parallel or antiparallel strand orientation of double helices. DNA and RNA duplexes in nature are exclusively antiparallel. Watson–Crick base-paired DNA or RNA helices display either right-handed or left-handed helical (pseudo-) symmetry. Genomic DNA is usually in the right-handed B-form, and RNA double helices adopt the right-handed A-conformation. Finally, there is a higher level of helical symmetry in superhelical DNA in which B-form double strands are intertwined in a right- or left-handed sense. Full article
(This article belongs to the Special Issue Symmetry in Molecular Biology)
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