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Computational Biophysics and Bioinformatics of Proteins
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Computational Biophysics and Bioinformatics of Proteins

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 November 2024) | Viewed by 2107

Special Issue Editor

Dr. Preeti Pandey

E-Mail Website
Guest Editor
Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
Interests: bioinformatics and computational biology; computational biology; protein structure; pathway analysis; computational systems biology; allosteric inhibition; drug discovery

Special Issue Information

Dear Colleagues,

Proteins are key players in various biological processes, so understanding their structure and function is essential for advancing our knowledge in fields such as fundamental biology, biomedicine, biotechnology/bioengineering, and drug discovery. While it is tempting to understand the elements of the biological system in its entirety as well as in isolation, understanding the structure, function, and dynamics of proteins and their interactions is of significant importance. Mutations and modifications like phosphorylation, ubiquitination, and other post-translational modifications further complicate protein regulation and function and add an additional level of complexity.

Through the use of computational biophysics and bioinformatics, researchers have been able to investigate the three-dimensional structure of proteins, predict their function, and analyze protein–ligand interactions. These computational methods have revolutionized the study of proteins by providing valuable insights into their structure and function and have emerged as important tools in the field of structural bioinformatics, complementing experimental efforts to characterize the vast protein universe.

This Special Issue of the International Journal of Molecular Sciences will focus on the “Computational Biophysics and Bioinformatics of Proteins”. In today’s rapidly advancing field of bioinformatics, computational biophysics and bioinformatics play a crucial role in understanding the complex structure, function, and dynamics of proteins. The research presented in this Special Issue will highlight the important role of computational biophysics and bioinformatics in advancing our understanding of protein structure and function.

We warmly welcome the submission of original research papers and reviews.

Dr. Preeti Pandey
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

  • protein
  • computational biophysics
  • bioinformatics
  • protein dynamics
  • protein–ligand binding
  • protein–protein interaction
  • proteins’ structure and function
  • drug discovery

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Published Papers (2 papers)

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Research

21 pages, 12701 KiB  
Article
The Dps Protein Protects Escherichia coli DNA in the Form of the Trimer
by Vladislav Kovalenko, Ksenia Tereshkina, Andrey Moiseenko, Yury L. Ryzhykau, Alexander I. Kuklin, Eduard Tereshkin, Petr Zaytsev, Anastasiya Generalova, Nadezhda Persiyantseva, Olga S. Sokolova, Yurii Krupyanskii and Nataliya Loiko
Int. J. Mol. Sci. 2025, 26(2), 619; https://doi.org/10.3390/ijms26020619 - 13 Jan 2025
Viewed by 420
Abstract
The Dps protein is the major DNA-binding protein of prokaryotes, which protects DNA during starvation by forming a crystalline complex. The structure of such an intracellular DNA-Dps complex is still unknown. However, the phenomenon of a decrease in the size of the Dps [...] Read more.
The Dps protein is the major DNA-binding protein of prokaryotes, which protects DNA during starvation by forming a crystalline complex. The structure of such an intracellular DNA-Dps complex is still unknown. However, the phenomenon of a decrease in the size of the Dps protein from 90 Å to 69–75 Å during the formation of a complex with DNA has been repeatedly observed, and no explanation has been given. In this work, we show that during the formation of intracellular DNA–Dps crystals, the protein transitions to another oligomeric form: from a dodecameric (of 12 monomers), which has an almost spherical shape with a diameter of 90 Å, to a trimeric (of three monomers), which has a shape close to a torus-like structure with a diameter of 70 Å and a height of 40 Å. The trimer model was obtained through the molecular dynamic modeling of the interaction of the three monomers of the Dps protein. Placement of the obtained trimer in the electron density of in vitro DNA–Dps crystal allowed for the determination of the lattice parameters of the studied crystal. This crystal model was in good agreement with the SAXS data obtained from intracellular crystals of 2-day-old Escherichia coli cells. The final crystal structure contains a DNA molecule in the through channel of the crystal structure between the Dps trimers. It was discussed that the mechanism of protein transition from one oligomeric form to another in the cell cytoplasm could be regulated by intracellular metabolites and is a simple and flexible mechanism of prokaryotic cell transition from one metabolic state to another. Full article
(This article belongs to the Special Issue Computational Biophysics and Bioinformatics of Proteins)
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16 pages, 291 KiB  
Article
AAindexNC: Estimating the Physicochemical Properties of Non-Canonical Amino Acids, Including Those Derived from the PDB and PDBeChem Databank
by Yury V. Milchevskiy, Galina I. Kravatskaya and Yury V. Kravatsky
Int. J. Mol. Sci. 2024, 25(23), 12555; https://doi.org/10.3390/ijms252312555 - 22 Nov 2024
Viewed by 614
Abstract
The physicochemical properties of amino acid residues from the AAindex database are widely used as predictors in building models for predicting both protein structures and properties. It should be noted, however, that the AAindex database contains data only for the 20 canonical amino [...] Read more.
The physicochemical properties of amino acid residues from the AAindex database are widely used as predictors in building models for predicting both protein structures and properties. It should be noted, however, that the AAindex database contains data only for the 20 canonical amino acids. Non-canonical amino acids, while less common, are not rare; the Protein Data Bank includes proteins with more than 1000 distinct non-canonical amino acids. In this study, we propose a method to evaluate the physicochemical properties from the AAindex database for non-canonical amino acids and assess the prediction quality. We implemented our method as a bioinformatics tool and estimated the physicochemical properties of non-canonical amino acids from the PDB with the chemical composition presentation using SMILES encoding obtained from the PDBechem databank. The bioinformatics tool and resulting database of the estimated properties are freely available on the author’s website and available for download via GitHub. Full article
(This article belongs to the Special Issue Computational Biophysics and Bioinformatics of Proteins)
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