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Symmetry
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Recent Advance in Biochemistry, Genetics and Molecular Biology
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Recent Advance in Biochemistry, Genetics and Molecular Biology

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

Deadline for manuscript submissions: closed (30 September 2022) | Viewed by 6900

Special Issue Editor

Dr. Dimitrios Vlachakis

E-Mail Website
Guest Editor
Genetics Laboratory, Biotechnology Department, Agricultural University of Athens, Athens, Greece
Interests: functional role of long non-coding RNAs; stress mechanisms and homeostasis via nuclear receptors; computational and molecular virology under the prisms of genetics; computational biology; precision medicine
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biochemistry, genetics, and molecular biology constitute an ever-changing field of modern biosciences. A lot of knowledge has been gained via basic research and strategies thereof have been designed with medical, biological, agricultural, and even environmental applications, starting from how basic biochemical reactions dictate the way in which cells operate, metabolize, and proliferate to advanced genetics or epigenetics of gene expression and regulation. New technology is continuously changing the scenery of modern biosciences and novel techniques allow the exploration of uncharted waters. For instance, who would have thought a few years ago that single-cell sequencing would be possible? The rate of knowledge acquisition, data collection, and innovation in the realm of biochemistry, genetics, and molecular biology has significantly increased, boosted, and fueled by the pandemic.

This Special Issue welcomes the submission of all articles stating or addressing recent advances in biochemistry, genetics, and molecular biology. This is a great opportunity to assemble and gather state-of-the-art research and review articles in a specialized depository that will serve as a world class reference to the abovementioned scientific field. Note that all submitted papers should be within the scope of the journal.

Prof. Dimitrios Vlachakis
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.

Published Papers (3 papers)

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Research

20 pages, 5298 KiB  
Article
Molecular Symmetry of Permethylated β-Cyclodextrins upon Complexation
by Kostas Bethanis, Elias Christoforides, Athena Andreou and Elias Eliopoulos
Symmetry 2022, 14(10), 2214; https://0-doi-org.brum.beds.ac.uk/10.3390/sym14102214 - 20 Oct 2022
Cited by 2 | Viewed by 1539
Abstract
The Cn molecular symmetry implicated by the schemes with which cyclodextrins (CDs), the well-known cyclic oligosaccharides, are introduced in the literature, is not valid. Numerous studies have shown that CDs are rather flexible with their macrocycle adopting various conformations that enable the [...] Read more.
The Cn molecular symmetry implicated by the schemes with which cyclodextrins (CDs), the well-known cyclic oligosaccharides, are introduced in the literature, is not valid. Numerous studies have shown that CDs are rather flexible with their macrocycle adopting various conformations that enable the inclusion complexation of guest molecules of various shapes. In this work, the loss and gain of the C7 symmetry of the heptakis (2, 3, 6-tri-O-methyl)-β-CD (TM-β-CD) is investigated by means of its conformation geometrical features in its hydrated form and upon complexation with molecules of different shapes. For this, the crystal structure of the inclusion complex of a bulky guest molecule (giberellic acid) in TM-β-CD is presented for the first time and compared with the previously determined crystal structures of monohydrated TM-β-CD and the inclusion complex of a linear monoterpenoid (geraniol) in TM-β-CD. The structural investigation was complemented by molecular dynamics simulations in an explicit solvent, based on the crystallographically determined models. The crucial role of the guest, in the symmetry gain of the host, reveals a pronounced induced-fit complexation mechanism for permethylated CDs. Full article
(This article belongs to the Special Issue Recent Advance in Biochemistry, Genetics and Molecular Biology)
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20 pages, 1821 KiB  
Article
Structural Characterization of Mono- and Dimethylphosphatidylethanolamines from Various Organisms Using a Complex Analytical Strategy including Chiral Chromatography
by Tomáš Řezanka, Andrea Palyzová, Milada Vítová, Tomáš Brányik, Markéta Kulišová and Jarošová Kolouchová Irena
Symmetry 2022, 14(3), 616; https://0-doi-org.brum.beds.ac.uk/10.3390/sym14030616 - 19 Mar 2022
Cited by 2 | Viewed by 1811
Abstract
Two minor phospholipids, i.e., mono- and/or dimethylphosphatidylethanolamines, are widespread in many organisms, from bacteria to higher plants and animals. A molecular mixture of methyl-PE and dimethyl-PE was obtained from total lipids by liquid chromatography and further identified by mass spectrometry. Total methyl-PE and [...] Read more.
Two minor phospholipids, i.e., mono- and/or dimethylphosphatidylethanolamines, are widespread in many organisms, from bacteria to higher plants and animals. A molecular mixture of methyl-PE and dimethyl-PE was obtained from total lipids by liquid chromatography and further identified by mass spectrometry. Total methyl-PE and dimethyl-PE were cleaved by phospholipase C, and the resulting diacylglycerols, in the form of acetyl derivatives, were separated into alkyl-acyl, alkenyl-acyl, and diacylglycerols. Reversed-phase LC/MS allowed dozens of molecular species to be identified and further analyzed. This was performed on a chiral column, and identification by tandem positive ESI revealed that diacyl derivatives from all four bacteria were mixtures of both R and S enantiomers. The same applied to alkenyl-acyl derivatives of anaerobic bacteria. Analysis thus confirmed that some bacteria biosynthesize phospholipids having both sn-glycerol-3-phosphate and sn-glycerol-1-phosphate as precursors. These findings were further supported by data already published in GenBank. The use of chiral chromatography made it possible to prove that both enantiomers of glycerol phosphate of some molecular species of mono- and dimethylphosphatidylethanolamines are present. The result of the analysis can be interpreted that the cultured bacteria do not have homochiral membranes but, on the contrary, have an asymmetric, i.e., heterochiral membranes. Full article
(This article belongs to the Special Issue Recent Advance in Biochemistry, Genetics and Molecular Biology)
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15 pages, 2803 KiB  
Article
Directed Evolution of a Glutathione Transferase for the Development of a Biosensor for Alachlor Determination
by Fereniki Perperopoulou, Maria Fragoulaki, Anastassios C. Papageorgiou and Nikolaos E. Labrou
Symmetry 2021, 13(3), 461; https://0-doi-org.brum.beds.ac.uk/10.3390/sym13030461 - 12 Mar 2021
Cited by 3 | Viewed by 2060
Abstract
In the present work, DNA recombination of three homologous tau class glutathione transferases (GSTUs) allowed the creation of a library of tau class GmGSTUs. The library was activity screened for the identification of glutathione transferase (GST) variants with enhanced catalytic activity towards [...] Read more.
In the present work, DNA recombination of three homologous tau class glutathione transferases (GSTUs) allowed the creation of a library of tau class GmGSTUs. The library was activity screened for the identification of glutathione transferase (GST) variants with enhanced catalytic activity towards the herbicide alachlor (2-chloro-2′,6′-diethyl-N-(methoxymethyl)acetanilide). One enzyme variant (GmGSTsf) with improved catalytic activity and binding affinity for alachlor was identified and explored for the development of an optical biosensor for alachlor determination. Kinetics analysis and molecular modeling studies revealed a key mutation (Ile69Val) at the subunit interface (helix α3) that appeared to be responsible for the altered catalytic properties. The enzyme was immobilized directly on polyvinylidenefluoride membrane by crosslinking with glutaraldehyde and was placed on the inner surface of a plastic cuvette. The rate of pH changes observed as a result of the enzyme reaction was followed optometrically using a pH indicator. A calibration curve indicated that the linear concentration range for alachlor was 30–300 μM. The approach used in the present study can provide tools for the generation of novel enzymes for eco-efficient and environment-friendly analytical technologies. In addition, the outcome of this study gives an example for harnessing protein symmetry for enzyme design. Full article
(This article belongs to the Special Issue Recent Advance in Biochemistry, Genetics and Molecular Biology)
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