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Journals
Biomolecules
Special Issues
Bioinformatics in Protein Evolution
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Bioinformatics in Protein Evolution

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Bioinformatics and Systems Biology".

Deadline for manuscript submissions: closed (15 December 2023) | Viewed by 5062

Special Issue Editors

Dr. Pablo Mier

E-Mail Website
Guest Editor
Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
Interests: bioinformatic; computational biology; proteins; low complexity regions; homorepeats; web tool development; biological databases; evolution
Dr. Lisanna Paladin

E-Mail Website
Guest Editor
Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
Interests: computational biology; proteins; software development; bioinformatics; protein structures; repeat proteins; protein features; evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The post-genomic era led to a huge and continuously increasing number of entries in protein databases. This, coupled with technologies allowing unprecedented annotation quality, provide the means to understand the evolution of protein families which are currently poorly described. For this Special Issue, we recruit manuscripts integrating bioinformatic analysis and discussing proteins’ evolution, either as a process or focused on specific motifs/domains. The use of data from multiple species or strains is highly recommended. We will discuss the multiple faces of molecular evolution, from sequences to structures to functions, leveraging on the recent developments in protein features prediction and system biology.

Dr. Pablo Mier
Dr. Lisanna Paladin
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. Biomolecules 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 2700 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

  • orthology/homology
  • protein families
  • sequence databases
  • sequence motifs
  • protein domains
  • phylogeny
  • bioinformatics
  • computational biology

Published Papers (2 papers)

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Research

9 pages, 1748 KiB  
Communication
Evolutionary Study of Protein Short Tandem Repeats in Protein Families
by Pablo Mier and Miguel A. Andrade-Navarro
Biomolecules 2023, 13(7), 1116; https://doi.org/10.3390/biom13071116 - 13 Jul 2023
Cited by 1 | Viewed by 949
Abstract
Tandem repeats in proteins are patterns of residues repeated directly adjacent to each other. The evolution of these repeats can be assessed by using groups of homologous sequences, which can help pointing to events of unit duplication or deletion. High pressure in a [...] Read more.
Tandem repeats in proteins are patterns of residues repeated directly adjacent to each other. The evolution of these repeats can be assessed by using groups of homologous sequences, which can help pointing to events of unit duplication or deletion. High pressure in a protein family for variation of a given type of repeat might point to their function. Here, we propose the analysis of protein families to calculate protein short tandem repeats (pSTRs) in each protein sequence and assess their variability within the family in terms of number of units. To facilitate this analysis, we developed the pSTR tool, a method to analyze the evolution of protein short tandem repeats in a given protein family by pairwise comparisons between evolutionarily related protein sequences. We evaluated pSTR unit number variation in protein families of 12 complete metazoan proteomes. We hypothesize that families with more dynamic ensembles of repeats could reflect particular roles of these repeats in processes that require more adaptability. Full article
(This article belongs to the Special Issue Bioinformatics in Protein Evolution)
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16 pages, 13956 KiB  
Article
xProtCAS: A Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures
by Hazem M. Kotb and Norman E. Davey
Biomolecules 2023, 13(6), 906; https://doi.org/10.3390/biom13060906 - 30 May 2023
Viewed by 3179
Abstract
The identification of protein surfaces required for interaction with other biomolecules broadens our understanding of protein function, their regulation by post-translational modification, and the deleterious effect of disease mutations. Protein interaction interfaces are often identifiable as patches of conserved residues on a protein’s [...] Read more.
The identification of protein surfaces required for interaction with other biomolecules broadens our understanding of protein function, their regulation by post-translational modification, and the deleterious effect of disease mutations. Protein interaction interfaces are often identifiable as patches of conserved residues on a protein’s surface. However, finding conserved accessible surfaces on folded regions requires an understanding of the protein structure to discriminate between functional and structural constraints on residue conservation. With the emergence of deep learning methods for protein structure prediction, high-quality structural models are now available for any protein. In this study, we introduce tools to identify conserved surfaces on AlphaFold2 structural models. We define autonomous structural modules from the structural models and convert these modules to a graph encoding residue topology, accessibility, and conservation. Conserved surfaces are then extracted using a novel eigenvector centrality-based approach. We apply the tool to the human proteome identifying hundreds of uncharacterised yet highly conserved surfaces, many of which contain clinically significant mutations. The xProtCAS tool is available as open-source Python software and an interactive web server. Full article
(This article belongs to the Special Issue Bioinformatics in Protein Evolution)
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