Approaches for the Reconstruction of Protein Families’ and Superfamilies’ Evolution with Consequences for De Novo Protein Design 2.0

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Biochemistry and Molecular Biology".

Deadline for manuscript submissions: 31 July 2024 | Viewed by 7496

Special Issue Editor


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Guest Editor
1. Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia
2. Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Wien, Austria
Interests: molecular phylogeny analysis; peroxidases; catalases; phylogenetic analysis; reactive oxygen species; oxidative stress
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Dear Colleagues,

I invite you to submit your original research work and reviews for the new issue of Biology (MDPI) with the title “Approaches for the Reconstruction of Protein Families’ and Superfamilies’ Evolution with Consequences for De Novo Protein Design 2.0. The focus of this updated issue topic is obtaining a comprehensive overview on various important achievements in the analysis of molecular evolution and structure–function relationships in diverse protein families and superfamilies originating from divergent organisms (both prokaryotic and eukaryotic). It will surely be interesting to compare convergent and divergent pathways of molecular evolution for distinct proteins based on experimental data and resolved 3D structures and to find out certain unifying rules. Additionally, the search for archetypal subfamilies and the sequences and structures of reconstructed ancestors is of great importance. This topic has already frequently been present in the literature of the last two decades, but the purpose of this Special Issue is to bring together current research outcomes from various experts and teams in one place to obtain a rather comprehensive overview of the capacity and possibilities of convergent and divergent modes of evolution within various protein folds for future perspectives of a targeted approach for de novo protein design.

Dr. Marcel Zamocky
Guest Editor

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Keywords

  • protein family evolution
  • protein superfamily
  • convergent evolution
  • divergent evolution
  • molecular phylogeny
  • horizontal gene transfer
  • structure–function relationship
  • de novo protein design

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Published Papers (3 papers)

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Research

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12 pages, 5722 KiB  
Article
The Molecular Evolution, Structure, and Function of Coproporphyrinogen Oxidase and Protoporphyrinogen Oxidase in Prokaryotes
by Marcel Zámocký, Stefan Hofbauer, Thomas Gabler and Paul G. Furtmüller
Biology 2023, 12(12), 1527; https://doi.org/10.3390/biology12121527 - 15 Dec 2023
Cited by 1 | Viewed by 1470
Abstract
Coproporphyrinogen oxidase (CgoX) and protoporphyrinogen oxidase (PgoX) catalyze the oxidation of the flexible cyclic tetrapyrrole of porphyrinogen compounds into fully conjugated, planar macrocyclic porphyrin compounds during heme biosynthesis. These enzymes are activated via different pathways. CgoX oxidizes coproporphyrinogen III to coproporphyrin III in [...] Read more.
Coproporphyrinogen oxidase (CgoX) and protoporphyrinogen oxidase (PgoX) catalyze the oxidation of the flexible cyclic tetrapyrrole of porphyrinogen compounds into fully conjugated, planar macrocyclic porphyrin compounds during heme biosynthesis. These enzymes are activated via different pathways. CgoX oxidizes coproporphyrinogen III to coproporphyrin III in the coproporphyrin-dependent pathway, whereas PgoX oxidizes protoporphyrinogen IX to protoporphyrin IX in the penultimate step of the protoporphyrin-dependent pathway. The phylogenetic analysis presented herein demonstrates a clear differentiation between the two enzyme classes, as evidenced by the clustering of sequences in distinct clades, and it shows that, at the origin of porphyrinogen-type oxidase evolution, PgoXs from cyanobacteria were found, which were noticeably separated from descendant PgoX representatives of Deltaproteobacteria and all later PgoX variants, leading to many eukaryotic clades. CgoX sequences originating from the monoderm Actinomycetota and Bacillota were well separated from the predecessor clades containing PgoX types and represent a peculiar type of gene speciation. The structural similarities and differences between these two oxidases are discussed based on their protein sequence alignment and a structural comparison. Full article
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25 pages, 4683 KiB  
Article
Ascorbate-Glutathione Cycle Genes Families in Euphorbiaceae: Characterization and Evolutionary Analysis
by Douglas Jardim-Messeder, Ygor de Souza-Vieira, Lucas Corrêa Lavaquial, Daniela Cassol, Vanessa Galhego, Gabriel Afonso Bastos, Thais Felix-Cordeiro, Régis Lopes Corrêa, Marcel Zámocký, Márcia Margis-Pinheiro and Gilberto Sachetto-Martins
Biology 2023, 12(1), 19; https://doi.org/10.3390/biology12010019 - 22 Dec 2022
Cited by 2 | Viewed by 2412
Abstract
Ascorbate peroxidase (APX), Monodehydroascorbate Reductase (MDAR), Dehydroascorbate Reductase (DHAR) and Glutathione Reductase (GR) enzymes participate in the ascorbate-glutathione cycle, which exerts a central role in the antioxidant metabolism in plants. Despite the importance of this antioxidant system in different signal transduction networks related [...] Read more.
Ascorbate peroxidase (APX), Monodehydroascorbate Reductase (MDAR), Dehydroascorbate Reductase (DHAR) and Glutathione Reductase (GR) enzymes participate in the ascorbate-glutathione cycle, which exerts a central role in the antioxidant metabolism in plants. Despite the importance of this antioxidant system in different signal transduction networks related to development and response to environmental stresses, the pathway has not yet been comprehensively characterized in many crop plants. Among different eudicotyledons, the Euphorbiaceae family is particularly diverse with some species highly tolerant to drought. Here the APX, MDAR, DHAR, and GR genes in Ricinus communis, Jatropha curcas, Manihot esculenta, and Hevea brasiliensis were identified and characterized. The comprehensive phylogenetic and genomic analyses allowed the classification of the genes into different classes, equivalent to cytosolic, peroxisomal, chloroplastic, and mitochondrial enzymes, and revealed the duplication events that contribute to the expansion of these families within plant genomes. Due to the high drought stress tolerance of Ricinus communis, the expression patterns of ascorbate-glutathione cycle genes in response to drought were also analyzed in leaves and roots, indicating a differential expression during the stress. Altogether, these data contributed to the characterization of the expression pattern and evolutionary analysis of these genes, filling the gap in the proposed functions of core components of the antioxidant mechanism during stress response in an economically relevant group of plants. Full article
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Review

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14 pages, 995 KiB  
Review
What Can De Novo Protein Design Bring to the Treatment of Hematological Disorders?
by Hui Lu, Zhipeng Cheng, Yu Hu and Liang V. Tang
Biology 2023, 12(2), 166; https://doi.org/10.3390/biology12020166 - 20 Jan 2023
Cited by 2 | Viewed by 2689
Abstract
Protein therapeutics have been widely used to treat hematological disorders. With the advent of de novo protein design, protein therapeutics are not limited to ameliorating natural proteins but also produce novel protein sequences, folds, and functions with shapes and functions customized to bind [...] Read more.
Protein therapeutics have been widely used to treat hematological disorders. With the advent of de novo protein design, protein therapeutics are not limited to ameliorating natural proteins but also produce novel protein sequences, folds, and functions with shapes and functions customized to bind to the therapeutic targets. De novo protein techniques have been widely used biomedically to design novel diagnostic and therapeutic drugs, novel vaccines, and novel biological materials. In addition, de novo protein design has provided new options for treating hematological disorders. Scientists have designed protein switches called Colocalization-dependent Latching Orthogonal Cage–Key pRoteins (Co-LOCKR) that perform computations on the surface of cells. De novo designed molecules exhibit a better capacity than the currently available tyrosine kinase inhibitors in chronic myeloid leukemia therapy. De novo designed protein neoleukin-2/15 enhances chimeric antigen receptor T-cell activity. This new technique has great biomedical potential, especially in exploring new treatment methods for hematological disorders. This review discusses the development of de novo protein design and its biological applications, with emphasis on the treatment of hematological disorders. Full article
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