Protein–Protein Interactions in Health and Disease

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Physiology and Pathology".

Deadline for manuscript submissions: closed (31 October 2023) | Viewed by 9513

Special Issue Editor

Institut Ruđer Bošković, Bijenička cesta 54, 10000 Zagreb, Croatia
Interests: p53 family of proteins; p53 isoforms; metastatic melanoma; protein interactions; BRAF inhibitors; resistance
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Special Issue Information

Dear Colleagues,

All biological systems within a cell are controlled by proteins. While some proteins act on their own, the vast majority of proteins associate physically with each other, forming protein–protein interactions (PPIs), to regulate normal cellular functions and to undertake new biological functions.

In a critical step toward unravelling these complex protein functions, studies on molecular relationships and the biology of the cell have been mapping the physical “interactions” between proteins. Many PPIs take place in a cell in a particular biomolecular context. Furthermore, PPIs are specific and can be both transient and stable. While stable interactions are necessary for protein complexes such as the hemoglobin ribosome, dynamic, brief interactions that modify the specific protein functions are transient and may lead to further alterations.

Therefore, an understanding of the physical contact between proteins in a cell is crucial for understanding cell physiology in normal and disease conditions. Many diseases, including cancer, are the result of the disruption of regular PPIs as well as aberrant PPIs, including endogenous cellular proteins and proteins from pathogens. Therefore, the reconstruction of regular or inhibition of aberrant interactions has significant clinical importance. PPIs can be affected by small molecules, some of which are already approved for clinical applications, therefore studying the nature of the PPIs is important for drug development.

Protein–protein interactions have been increasingly studied using several approaches, and the obtained information enables the establishment of large protein interaction networks. The PPIs contribute to the interactome, the collection of molecular interactions that occur either in a cell, in an organism or in a specific biological context. Due to the development of large-scale, high-throughput screening techniques, we are able to obtain an immense quantity of data which are available in databases and could have therapeutic importance.

Dr. Neda Slade
Guest Editor

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Keywords

  • protein–protein interactions
  • protein complex
  • protein–protein interactions inhibitors
  • protein networks
  • interactome

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Published Papers (3 papers)

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Research

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10 pages, 1207 KiB  
Communication
Detection of Recombinant Proteins SOX2 and OCT4 Interacting in HEK293T Cells Using Real-Time Quantitative PCR
by Darkhan Kanayev, Diana Abilmazhenova, Ilyas Akhmetollayev, Aliya Sekenova, Vyacheslav Ogay and Arman Kulyyassov
Life 2023, 13(1), 107; https://doi.org/10.3390/life13010107 - 30 Dec 2022
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Abstract
In vivo biotinylation using wild-type and mutants of biotin ligases is now widely applied for the study of cellular proteomes. The commercial availability of kits for the highly efficient purification of biotinylated proteins and their excellent compatibility with LC-MS/MS protocols are the main [...] Read more.
In vivo biotinylation using wild-type and mutants of biotin ligases is now widely applied for the study of cellular proteomes. The commercial availability of kits for the highly efficient purification of biotinylated proteins and their excellent compatibility with LC-MS/MS protocols are the main reasons for the choice of biotin ligases. Since they are all enzymes, however, just a very low expression in cells is required for experiments. Therefore, it can be difficult to perform the quantifications of these enzymes in various samples. Traditional methods, such as western blotting, are not always fit for the detection of the expression levels. Therefore, real-time qRT-PCR, a technology that is more sensitive, was used in this study to quantify the expression of BirA fusions. Using this method, we detected high expression levels of BirA fusions in models of interactions of pluripotency transcription factors to carry out their relative quantification. We also found the absence of the competing endogenous proteins SOX2 and OCT4, as well as no cross-reactivity between BAP/BirA and the endogenous biotinylation system in HEK293T cells. Thus, these data indicated that the high level of biotinylation is due to the in vivo interaction of BAP-X and BirA-Y (X,Y = SOX2, OCT4) in the cell rather than their random collision, a big difference in the expression level of BirA fusions across samples or endogenous biotinylation. Full article
(This article belongs to the Special Issue Protein–Protein Interactions in Health and Disease)
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14 pages, 1346 KiB  
Article
Generation of Peptides for Highly Efficient Proximity Utilizing Site-Specific Biotinylation in Cells
by Arman Kulyyassov, Yerlan Ramankulov and Vasily Ogryzko
Life 2022, 12(2), 300; https://doi.org/10.3390/life12020300 - 16 Feb 2022
Cited by 3 | Viewed by 3127
Abstract
Protein tags are peptide sequences genetically embedded into a recombinant protein for various purposes, such as affinity purification, Western blotting, and immunofluorescence. Another recent application of peptide tags is in vivo labeling and analysis of protein–protein interactions (PPI) by proteomics methods. One of [...] Read more.
Protein tags are peptide sequences genetically embedded into a recombinant protein for various purposes, such as affinity purification, Western blotting, and immunofluorescence. Another recent application of peptide tags is in vivo labeling and analysis of protein–protein interactions (PPI) by proteomics methods. One of the common workflows involves site-specific in vivo biotinylation of an AviTag-fused protein in the presence of the biotin ligase BirA. However, due to the rapid kinetics of labeling, this tag is not ideal for analysis of PPI. Here we describe the rationale, design, and protocol for the new biotin acceptor peptides BAP1070 and BAP1108 using modular assembling of biotin acceptor fragments, DNA sequencing, transient expression of proteins in cells, and Western blotting methods. These tags were used in the Proximity Utilizing Biotinylation (PUB) method, which is based on coexpression of BAP-X and BirA-Y in mammalian cells, where X or Y are candidate interacting proteins of interest. By changing the sequence of these peptides, a low level of background biotinylation is achieved, which occurs due to random collisions of proteins in cells. Over 100 plasmid constructs, containing genes of transcription factors, histones, gene repressors, and other nuclear proteins were obtained during implementation of projects related to this method. Full article
(This article belongs to the Special Issue Protein–Protein Interactions in Health and Disease)
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Review

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23 pages, 1358 KiB  
Review
Protein–Protein Interactions of Seryl-tRNA Synthetases with Emphasis on Human Counterparts and Their Connection to Health and Disease
by Morana Dulic, Vlatka Godinic-Mikulcic, Mario Kekez, Valentina Evic and Jasmina Rokov-Plavec
Life 2024, 14(1), 124; https://doi.org/10.3390/life14010124 - 15 Jan 2024
Cited by 1 | Viewed by 2906
Abstract
Seryl-tRNA synthetases (SerRSs), members of the aminoacyl-tRNA synthetase family, interact with diverse proteins, enabling SerRSs to enhance their role in the translation of the genetic message or to perform alternative functions in cellular processes beyond translation. Atypical archaeal SerRS interacts with arginyl-tRNA synthetase [...] Read more.
Seryl-tRNA synthetases (SerRSs), members of the aminoacyl-tRNA synthetase family, interact with diverse proteins, enabling SerRSs to enhance their role in the translation of the genetic message or to perform alternative functions in cellular processes beyond translation. Atypical archaeal SerRS interacts with arginyl-tRNA synthetase and proteins of the ribosomal P-stalk to optimize translation through tRNA channeling. The complex between yeast SerRS and peroxin Pex21p provides a connection between translation and peroxisome function. The partnership between Arabidopsis SerRS and BEN1 indicates a link between translation and brassinosteroid metabolism and may be relevant in plant stress response mechanisms. In Drosophila, the unusual heterodimeric mitochondrial SerRS coordinates mitochondrial translation and replication via interaction with LON protease. Evolutionarily conserved interactions of yeast and human SerRSs with m3C32 tRNA methyltransferases indicate coordination between tRNA modification and aminoacylation in the cytosol and mitochondria. Human cytosolic SerRS is a cellular hub protein connecting translation to vascular development, angiogenesis, lipogenesis, and telomere maintenance. When translocated to the nucleus, SerRS acts as a master negative regulator of VEGFA gene expression. SerRS alone or in complex with YY1 and SIRT2 competes with activating transcription factors NFκB1 and c-Myc, resulting in balanced VEGFA expression important for proper vascular development and angiogenesis. In hypoxia, SerRS phosphorylation diminishes its binding to the VEGFA promoter, while the lack of nutrients triggers SerRS glycosylation, reducing its nuclear localization. Additionally, SerRS binds telomeric DNA and cooperates with the shelterin protein POT1 to regulate telomere length and cellular senescence. As an antitumor and antiangiogenic factor, human cytosolic SerRS appears to be a promising drug target and therapeutic agent for treating cancer, cardiovascular diseases, and possibly obesity and aging. Full article
(This article belongs to the Special Issue Protein–Protein Interactions in Health and Disease)
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