International Journal of Molecular Sciences

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Special Issue Editor

Prof. Dr. Tamara M. Khlebodarova

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Guest Editor

Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
Interests: molecular genetic and metabolic systems; modeling; complex dynamics

Special Issue Information

Dear Colleagues,

This Special Issue is devoted to the structural and dynamic characteristics of molecular systems from a biological perspective. It will cover the various levels of their organization, from individual biomolecules (metabolites, proteins, RNA and DNA) to molecular genetic networks (metabolic pathways, gene regulatory networks and gene association networks) formed through physical or functional interactions. An interdisciplinary approach to the topology and dynamics of molecular networks, including the structural and dynamic properties of their component macromolecules, opens the way for understanding the complex mechanisms underlying the functioning of living systems. This Special Issue’s ultimate goal is to discuss the molecular mechanisms of biological processes and how their disruption contributes to various conditions, such as disease and the response to internal and external factors.

This Special Issue covers original research and reviews featuring interdisciplinary approaches such as structural biology, omics data analysis (metabolomic, proteomic, genomic, transcriptomic, etc.), and network analysis and modeling that contribute to the molecular and biological systems research community.

Since IJMS is a journal of molecular science, pure clinical studies are not suitable for our journal. However, clinical or pure model submissions with biomolecular experiments are welcome.

I warmly welcome your contributions to this Special Issue of “The Structural and Dynamical Characterization of Biological Processes".

Prof. Dr. Tamara M. Khlebodarova
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

structural and functional organization of macromolecules and molecular systems
metabolic pathways
regulatory networks of genes
associative networks of genes
modeling
metabolomics
proteomic and transcriptomic data

Published Papers (2 papers)

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Research

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13 pages, 2616 KiB

Open AccessArticle

Impact of Negative Feedbacks on De Novo Pyrimidines Biosynthesis in Escherichia coli

by Ilya R. Akberdin, Konstantin N. Kozlov, Fedor V. Kazantsev, Stanislav I. Fadeev, Vitaly A. Likhoshvai and Tamara M. Khlebodarova

Int. J. Mol. Sci. 2023, 24(5), 4806; https://doi.org/10.3390/ijms24054806 - 02 Mar 2023

Cited by 2 | Viewed by 1311

Abstract

Earlier studies aimed at investigating the metabolism of endogenous nucleoside triphosphates in synchronous cultures of E. coli cells revealed an auto-oscillatory mode of functioning of the pyrimidine and purine nucleotide biosynthesis system, which the authors associated with the dynamics of cell division. Theoretically, this system has an intrinsic oscillatory potential, since the dynamics of its functioning are controlled through feedback mechanisms. The question of whether the nucleotide biosynthesis system has its own oscillatory circuit is still open. To address this issue, an integral mathematical model of pyrimidine biosynthesis was developed, taking into account all experimentally verified negative feedback in the regulation of enzymatic reactions, the data of which were obtained under in vitro conditions. Analysis of the dynamic modes of the model functioning has shown that in the pyrimidine biosynthesis system, both the steady-state and oscillatory functioning modes can be realized under certain sets of kinetic parameters that fit in the physiological boundaries of the investigated metabolic system. It has been demonstrated that the occurrence of the oscillatory nature of metabolite synthesis depended on the ratio of two parameters: the Hill coefficient, h_UMP1—the nonlinearity of the UMP effect on the activity of carbamoyl-phosphate synthetase, and the parameter r characterizing the contribution of the noncompetitive mechanism of UTP inhibition to the regulation of the enzymatic reaction of UMP phosphorylation. Thus, it has been theoretically shown that the E. coli pyrimidine biosynthesis system possesses its own oscillatory circuit whose oscillatory potential depends to a significant degree on the mechanism of regulation of UMP kinase activity. Full article

(This article belongs to the Special Issue The Structural and Dynamical Characterization of Biological Processes)

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Review

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19 pages, 5771 KiB

Open AccessReview

The Evolution of Life Is a Road Paved with the DNA Quadruplet Symmetry and the Supersymmetry Genetic Code

by Marija Rosandić and Vladimir Paar

Int. J. Mol. Sci. 2023, 24(15), 12029; https://doi.org/10.3390/ijms241512029 - 27 Jul 2023

Cited by 2 | Viewed by 1455

Abstract

Symmetries have not been completely determined and explained from the discovery of the DNA structure in 1953 and the genetic code in 1961. We show, during 10 years of investigation and research, our discovery of the Supersymmetry Genetic Code table in the form of 2 × 8 codon boxes, quadruplet DNA symmetries, and the classification of trinucleotides/codons, all built with the same physiochemical double mirror symmetry and Watson–Crick pairing. We also show that single-stranded RNA had the complete code of life in the form of the Supersymmetry Genetic Code table simultaneously with instructions of codons’ relationship as to how to develop the DNA molecule on the principle of Watson–Crick pairing. We show that the same symmetries between the genetic code and DNA quadruplet are highly conserved during the whole evolution even between phylogenetically distant organisms. In this way, decreasing disorder and entropy enabled the evolution of living beings up to sophisticated species with cognitive features. Our hypothesis that all twenty amino acids are necessary for the origin of life on the Earth, which entirely changes our view on evolution, confirms the evidence of organic natural amino acids from the extra-terrestrial asteroid Ryugu, which is nearly as old as our solar system. Full article

(This article belongs to the Special Issue The Structural and Dynamical Characterization of Biological Processes)

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