Catalytic Receptors and Enzymes Involved in Cell-Signaling and Control

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Enzymology".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 4137

Special Issue Editor


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Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Tykistökatu 6A, 20520 Turku, Finland
Interests: structure-function relationships; structural bioinformatics; structure modeling; ligand binding and function; protein evolution; effects of mutations; EGFR family of tyrosine kinases; integrins; GPCRs; PDR-like family of transcription factors; calcium binding proteins; proteases
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Special Issue Information

Dear Colleagues,

Enzymes play a large variety of essential roles in an organism, facilitating the chemical reactions necessary for life’s processes. In this Special Issue, we aim to attract articles from a wide scope of studies that explore, e.g., the structure, biochemical, and biological consequences of enzyme functions in health, disease, and also biotechnological applications. Because of their key biochemical roles and localized binding sites for small molecules and macromolecules, enzymes are often targets of inhibitor drugs in medicine and as tools for probing function. Moreover, regulatory enzymes are frequently subject to somatic mutations, most often innocuous, but some mutations elicit functional changes that significantly alter enzymatic activity and ligand binding, affecting health as well as clinical treatment with pharmaceuticals. We would like to address enzymes that play key roles in regulating cellular processes as part of enzyme-linked receptors, enzymes functioning in post-translational modifications, and enzymes functioning through other controlling and regulatory mechanisms acting on molecular processes and cellular signaling.

Prof. Dr. Mark S. Johnson
Guest Editor

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Keywords

  • regulatory enzymes
  • enzyme-linked receptors, tyrosine kinase receptor families
  • serine/threonine kinases
  • post-translational modifications
  • enzyme structure, function, somatic mutations, molecular interactions, ligand recognition

Published Papers (2 papers)

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Research

13 pages, 1918 KiB  
Article
Proteome-Wide Detection and Annotation of Receptor Tyrosine Kinases (RTKs): RTK-PRED and the TyReK Database
by Georgios Filis, Fotis A. Baltoumas, Georgios Spanogiannis, Zoi I. Litou and Vassiliki A. Iconomidou
Biomolecules 2023, 13(2), 270; https://doi.org/10.3390/biom13020270 - 1 Feb 2023
Cited by 1 | Viewed by 1836
Abstract
Receptor tyrosine kinases (RTKs) form a highly important group of protein receptors of the eukaryotic cell membrane. They control many vital cellular functions and are involved in the regulation of complex signaling networks. Mutations in RTKs have been associated with different types of [...] Read more.
Receptor tyrosine kinases (RTKs) form a highly important group of protein receptors of the eukaryotic cell membrane. They control many vital cellular functions and are involved in the regulation of complex signaling networks. Mutations in RTKs have been associated with different types of cancers and other diseases. Although they are very important for proper cell function, they have been experimentally studied in a limited range of eukaryotic species. Currently, there is no available database for RTKs providing information about their function, expression, and interactions. Therefore, the identification of RTKs in multiple organisms, the documentation of their characteristics, and the collection of related information would be very useful. In this paper, we present a novel RTK detection pipeline (RTK-PRED) and the Receptor Tyrosine Kinases Database (TyReK-DB). RTK-PRED combines profile HMMs with transmembrane topology prediction to identify and classify potential RTKs. Proteins of all eukaryotic reference proteomes of the UniProt database were used as input in RTK-PRED leading to a filtered dataset of 20,478 RTKs. Based on the information collected for these RTKs from multiple databases, the relational TyReK database was created. Full article
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23 pages, 5678 KiB  
Article
An Evolutionary Perspective on the Origin, Conservation and Binding Partner Acquisition of Tankyrases
by Sven T. Sowa, Chiara Bosetti, Albert Galera-Prat, Mark S. Johnson and Lari Lehtiö
Biomolecules 2022, 12(11), 1688; https://doi.org/10.3390/biom12111688 - 15 Nov 2022
Cited by 2 | Viewed by 1851
Abstract
Tankyrases are poly-ADP-ribosyltransferases that regulate many crucial and diverse cellular processes in humans such as Wnt signaling, telomere homeostasis, mitotic spindle formation and glucose metabolism. While tankyrases are present in most animals, functional differences across species may exist. In this work, we confirm [...] Read more.
Tankyrases are poly-ADP-ribosyltransferases that regulate many crucial and diverse cellular processes in humans such as Wnt signaling, telomere homeostasis, mitotic spindle formation and glucose metabolism. While tankyrases are present in most animals, functional differences across species may exist. In this work, we confirm the widespread distribution of tankyrases throughout the branches of multicellular animal life and identify the single-celled choanoflagellates as earliest origin of tankyrases. We further show that the sequences and structural aspects of TNKSs are well-conserved even between distantly related species. We also experimentally characterized an anciently diverged tankyrase homolog from the sponge Amphimedon queenslandica and show that the basic functional aspects, such as poly-ADP-ribosylation activity and interaction with the canonical tankyrase binding peptide motif, are conserved. Conversely, the presence of tankyrase binding motifs in orthologs of confirmed interaction partners varies greatly between species, indicating that tankyrases may have different sets of interaction partners depending on the animal lineage. Overall, our analysis suggests a remarkable degree of conservation for tankyrases, and that their regulatory functions in cells have likely changed considerably throughout evolution. Full article
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