Expanding the potential genes of inborn errors of immunity through protein interactions

Abstract Background Inborn errors of immunity (IEI) are a group of genetic disorders that impair the immune system, with over 400 genes described so far, and hundreds more to be discovered. To facilitate the search for new genes, we need a way to prioritize among all the genes in the genome those most likely to play an important role in immunity. Results Here we identify a new list of genes by linking known IEI genes to new ones by using open-source databases of protein-protein interactions, post-translational modifications, and transcriptional regulation. We analyze this new set of 2,530 IEI-related genes for their tolerance of genetic variation and by their expression levels in various immune cell types. Conclusions By merging genes derived from protein interactions of known IEI genes with transcriptional data, we offer a new list of candidate genes that may play a role in as-yet undiscovered IEIs.

Download Full-text

Expanding the Potential Genes of Inborn Errors of Immunity through Protein Interactions

10.1101/2021.05.10.443508 ◽

2021 ◽

Author(s):

Humza A Khan ◽

Manish J Butte

Keyword(s):

Genetic Variation ◽

Protein Interactions ◽

Immune Cell ◽

Genetic Disorders ◽

Cell Types ◽

Protein Protein Interactions ◽

Inborn Errors ◽

Post Translational Modifications ◽

New Genes ◽

Inborn Errors Of Immunity

Inborn errors of immunity (IEI) are a group of genetic disorders that impair the immune system, with over 400 genes described so far, and hundreds more to be discovered. To facilitate the search for new genes, we need a way to prioritize among all the genes in the genome those most likely to play an important role in immunity. Here we identify a new list of genes by linking known IEI genes to new ones by using open-source databases of protein-protein interactions, post-translational modifications, and transcriptional regulation. We analyze this new set of 2,530 IEI-related genes for their tolerance of genetic variation and by their expression levels in various immune cell types.

Download Full-text

Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling

Nature Communications ◽

10.1038/s41467-021-27639-0 ◽

2022 ◽

Vol 13 (1) ◽

Author(s):

Jana Zecha ◽

Wassim Gabriel ◽

Ria Spallek ◽

Yun-Chien Chang ◽

Julia Mergner ◽

...

Keyword(s):

Protein Interactions ◽

Protein Turnover ◽

Isotope Labeling ◽

Cell Types ◽

Protein Protein Interactions ◽

Post Translational Modifications ◽

Online Tool ◽

Native Proteins ◽

Stability Structure ◽

The Impact

AbstractProteome-wide measurements of protein turnover have largely ignored the impact of post-translational modifications (PTMs). To address this gap, we employ stable isotope labeling and mass spectrometry to measure the turnover of >120,000 peptidoforms including >33,000 phosphorylated, acetylated, and ubiquitinated peptides for >9,000 native proteins. This site-resolved protein turnover (SPOT) profiling discloses global and site-specific differences in turnover associated with the presence or absence of PTMs. While causal relationships may not always be immediately apparent, we speculate that PTMs with diverging turnover may distinguish states of differential protein stability, structure, localization, enzymatic activity, or protein-protein interactions. We show examples of how the turnover data may give insights into unknown functions of PTMs and provide a freely accessible online tool that allows interrogation and visualisation of all turnover data. The SPOT methodology is applicable to many cell types and modifications, offering the potential to prioritize PTMs for future functional investigations.

Download Full-text

Faculty Opinions recommendation of A tethered catalysis, two-hybrid system to identify protein-protein interactions requiring post-translational modifications.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1020074.241459 ◽

2004 ◽

Author(s):

Igor Stagljar

Keyword(s):

Hybrid System ◽

Protein Interactions ◽

Protein Protein Interactions ◽

Post Translational Modifications ◽

Two Hybrid

Download Full-text

Protein Interaction Domains and Post-Translational Modifications: Structural Features and Drug Discovery Applications

Current Medicinal Chemistry ◽

10.2174/0929867326666190620101637 ◽

2020 ◽

Vol 27 (37) ◽

pp. 6306-6355 ◽

Cited By ~ 2

Author(s):

Marian Vincenzi ◽

Flavia Anna Mercurio ◽

Marilisa Leone

Keyword(s):

Drug Discovery ◽

Protein Interaction ◽

Protein Interactions ◽

Structural Information ◽

Protein Complexes ◽

Structural Features ◽

Protein Protein Interactions ◽

Modular Architecture ◽

Post Translational Modifications ◽

Interaction Domains

Background:: Many pathways regarding healthy cells and/or linked to diseases onset and progression depend on large assemblies including multi-protein complexes. Protein-protein interactions may occur through a vast array of modules known as protein interaction domains (PIDs). Objective:: This review concerns with PIDs recognizing post-translationally modified peptide sequences and intends to provide the scientific community with state of art knowledge on their 3D structures, binding topologies and potential applications in the drug discovery field. Method:: Several databases, such as the Pfam (Protein family), the SMART (Simple Modular Architecture Research Tool) and the PDB (Protein Data Bank), were searched to look for different domain families and gain structural information on protein complexes in which particular PIDs are involved. Recent literature on PIDs and related drug discovery campaigns was retrieved through Pubmed and analyzed. Results and Conclusion:: PIDs are rather versatile as concerning their binding preferences. Many of them recognize specifically only determined amino acid stretches with post-translational modifications, a few others are able to interact with several post-translationally modified sequences or with unmodified ones. Many PIDs can be linked to different diseases including cancer. The tremendous amount of available structural data led to the structure-based design of several molecules targeting protein-protein interactions mediated by PIDs, including peptides, peptidomimetics and small compounds. More studies are needed to fully role out, among different families, PIDs that can be considered reliable therapeutic targets, however, attacking PIDs rather than catalytic domains of a particular protein may represent a route to obtain selective inhibitors.

Download Full-text

Interactome Analysis of KIN (Kin17) Shows New Functions of This Protein

Current Issues in Molecular Biology ◽

10.3390/cimb43020056 ◽

2021 ◽

Vol 43 (2) ◽

pp. 767-781

Author(s):

Vanessa Pinatto Gaspar ◽

Anelise Cardoso Ramos ◽

Philippe Cloutier ◽

José Renato Pattaro Junior ◽

Francisco Ferreira Duarte Junior ◽

...

Keyword(s):

Dna Replication ◽

Protein Interactions ◽

Ribosome Biogenesis ◽

Cell Metabolism ◽

Cell Types ◽

Protein Protein Interactions ◽

Cellular Mechanisms ◽

Cancerous Cell ◽

First Time

KIN (Kin17) protein is overexpressed in a number of cancerous cell lines, and is therefore considered a possible cancer biomarker. It is a well-conserved protein across eukaryotes and is ubiquitously expressed in all cell types studied, suggesting an important role in the maintenance of basic cellular function which is yet to be well determined. Early studies on KIN suggested that this nuclear protein plays a role in cellular mechanisms such as DNA replication and/or repair; however, its association with chromatin depends on its methylation state. In order to provide a better understanding of the cellular role of this protein, we investigated its interactome by proximity-dependent biotin identification coupled to mass spectrometry (BioID-MS), used for identification of protein–protein interactions. Our analyses detected interaction with a novel set of proteins and reinforced previous observations linking KIN to factors involved in RNA processing, notably pre-mRNA splicing and ribosome biogenesis. However, little evidence supports that this protein is directly coupled to DNA replication and/or repair processes, as previously suggested. Furthermore, a novel interaction was observed with PRMT7 (protein arginine methyltransferase 7) and we demonstrated that KIN is modified by this enzyme. This interactome analysis indicates that KIN is associated with several cell metabolism functions, and shows for the first time an association with ribosome biogenesis, suggesting that KIN is likely a moonlight protein.

Download Full-text

Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions

PLoS Computational Biology ◽

10.1371/journal.pcbi.1008988 ◽

2021 ◽

Vol 17 (5) ◽

pp. e1008988

Author(s):

Nikolina ŠoŠtarić ◽

Vera van Noort

Keyword(s):

Molecular Dynamics ◽

Conformational Changes ◽

Protein Interactions ◽

Protein Structures ◽

Cellular Protein ◽

Free Energy Calculations ◽

Protein Protein Interactions ◽

Post Translational Modifications ◽

Protein Properties ◽

Dynamics Simulations

Post-translational modifications (PTMs) play a vital, yet often overlooked role in the living cells through modulation of protein properties, such as localization and affinity towards their interactors, thereby enabling quick adaptation to changing environmental conditions. We have previously benchmarked a computational framework for the prediction of PTMs’ effects on the stability of protein-protein interactions, which has molecular dynamics simulations followed by free energy calculations at its core. In the present work, we apply this framework to publicly available data on Saccharomyces cerevisiae protein structures and PTM sites, identified in both normal and stress conditions. We predict proteome-wide effects of acetylations and phosphorylations on protein-protein interactions and find that acetylations more frequently have locally stabilizing roles in protein interactions, while the opposite is true for phosphorylations. However, the overall impact of PTMs on protein-protein interactions is more complex than a simple sum of local changes caused by the introduction of PTMs and adds to our understanding of PTM cross-talk. We further use the obtained data to calculate the conformational changes brought about by PTMs. Finally, conservation of the analyzed PTM residues in orthologues shows that some predictions for yeast proteins will be mirrored to other organisms, including human. This work, therefore, contributes to our overall understanding of the modulation of the cellular protein interaction networks in yeast and beyond.

Download Full-text

Aspartic Acid Isomerization Characterized by High Definition Mass Spectrometry Significantly Alters the Bioactivity of a Novel Toxin from Poecilotheria

Toxins ◽

10.3390/toxins12040207 ◽

2020 ◽

Vol 12 (4) ◽

pp. 207 ◽

Cited By ~ 1

Author(s):

Stephen R. Johnson ◽

Hillary G. Rikli

Keyword(s):

Mass Spectrometry ◽

Protein Interactions ◽

Ion Mobility ◽

Protein Protein Interactions ◽

High Definition ◽

Vast Number ◽

Post Translational Modifications ◽

C Terminus ◽

Acid Isomerization

Research in toxinology has created a pharmacological paradox. With an estimated 220,000 venomous animals worldwide, the study of peptidyl toxins provides a vast number of effector molecules. However, due to the complexity of the protein-protein interactions, there are fewer than ten venom-derived molecules on the market. Structural characterization and identification of post-translational modifications are essential to develop biological lead structures into pharmaceuticals. Utilizing advancements in mass spectrometry, we have created a high definition approach that fuses conventional high-resolution MS-MS with ion mobility spectrometry (HDMSE) to elucidate these primary structure characteristics. We investigated venom from ten species of “tiger” spider (Genus: Poecilotheria) and discovered they contain isobaric conformers originating from non-enzymatic Asp isomerization. One conformer pair conserved in five of ten species examined, denominated PcaTX-1a and PcaTX-1b, was found to be a 36-residue peptide with a cysteine knot, an amidated C-terminus, and isoAsp33Asp substitution. Although the isomerization of Asp has been implicated in many pathologies, this is the first characterization of Asp isomerization in a toxin and demonstrates the isomerized product’s diminished physiological effects. This study establishes the value of a HDMSE approach to toxin screening and characterization.

Download Full-text

A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field

Proteomes ◽

10.3390/proteomes8030014 ◽

2020 ◽

Vol 8 (3) ◽

pp. 14 ◽

Cited By ~ 4

Author(s):

Emmalyn J. Dupree ◽

Madhuri Jayathirtha ◽

Hannah Yorkey ◽

Marius Mihasan ◽

Brindusa Alina Petre ◽

...

Keyword(s):

Data Analysis ◽

Sample Preparation ◽

Protein Interactions ◽

Clinical Setting ◽

Critical Review ◽

Basic Science ◽

Protein Protein Interactions ◽

Bottom Up ◽

Post Translational Modifications ◽

The Future

Proteomics is the field of study that includes the analysis of proteins, from either a basic science prospective or a clinical one. Proteins can be investigated for their abundance, variety of proteoforms due to post-translational modifications (PTMs), and their stable or transient protein–protein interactions. This can be especially beneficial in the clinical setting when studying proteins involved in different diseases and conditions. Here, we aim to describe a bottom-up proteomics workflow from sample preparation to data analysis, including all of its benefits and pitfalls. We also describe potential improvements in this type of proteomics workflow for the future.

Download Full-text

Jasmonate and auxin perception: how plants keep F-boxes in check

Journal of Experimental Botany ◽

10.1093/jxb/erz272 ◽

2019 ◽

Vol 70 (13) ◽

pp. 3401-3414 ◽

Cited By ~ 5

Author(s):

Clara Williams ◽

Patricia Fernández-Calvo ◽

Maite Colinas ◽

Laurens Pauwels ◽

Alain Goossens

Keyword(s):

Protein Interactions ◽

26S Proteasome ◽

Protein Protein Interactions ◽

Biotic And Abiotic Stresses ◽

Post Translational Modifications ◽

Receptor Complexes ◽

Subsequent Degradation ◽

Selective Agonists ◽

Multiple Levels ◽

Type Receptor

Abstract Phytohormones regulate the plasticity of plant growth and development, and responses to biotic and abiotic stresses. Many hormone signal transduction cascades involve ubiquitination and subsequent degradation of proteins by the 26S proteasome. The conjugation of ubiquitin to a substrate is facilitated by the E1 activating, E2 conjugating, and the substrate-specifying E3 ligating enzymes. The most prevalent type of E3 ligase in plants is the Cullin–RING ligase (CRL)-type, with F-box proteins (FBPs) as the substrate recognition component. The activity of these SKP–Cullin–F-box (SCF) complexes needs to be tightly regulated in time and place. Here, we review the regulation of SCF function in plants on multiple levels, with a focus on the auxin and jasmonate SCF-type receptor complexes. We discuss in particular the relevance of protein–protein interactions and post-translational modifications as mechanisms to keep SCF functioning under control. Additionally, we highlight the unique property of SCFTIR1/AFB and SCFCOI1 to recognize substrates by forming co-receptor complexes. Finally, we explore how engineered selective agonists can be used to study and uncouple the outcomes of the complex auxin and jasmonate signaling networks that are governed by these FBPs.

Download Full-text