Competition-cooperation relationship networks characterize the competition and cooperation between proteins

Hong, Li; Zhou, Yuan; Zhang, Ziding

doi:10.1038/srep11619

Cited by 4 publications

(4 citation statements)

References 46 publications

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“…Those results could be reproduced over a range of thresholds for binding site overlap definition ( Supplementary Figure S4 ). The reason could be that alternative regulatory mechanisms prevent competition between partners ( Li et al, 2015 ) or that our computational estimates of competition vs. cooperative binding are not accurate. For example, biophysical properties of interaction sites of proteins (e.g., steric hindrance) can favor or prevent interactions between them and thus, the classification of proteins based on the overlap in the interaction interface might not represent competitive or cooperative binding in reality.…”

Section: Discussionmentioning

confidence: 99%

Protein Complex Organization Imposes Constraints on Proteome Dysregulation in Cancer

Senger

Schaefer

2021

Front. Bioinform.

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Protein assembly is a highly dynamic process and proteins can interact in different ways and stoichiometries within a complex. The importance of maintaining protein stoichiometry for complex function and avoiding aggregation of orphan subunits has been demonstrated. However, how exactly the organization of proteins into complexes constrains differential protein abundance in extreme cellular conditions like cancer, where a lot of protein abundance changes occur, has not been systematically investigated. To study this, we collected proteomic data made available by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) to quantify proteomic changes during carcinogenesis and systematically tested five interaction types in complexes to investigate which of these features impact on protein abundance correlation patterns in cancer. We found that higher than expected fraction of protein complex subunits does not show changes in their abundances compared to those in the normal samples. Furthermore, we found that the way proteins interact in complexes indeed constrains their co-abundance patterns. Our results highlight the role of the interactions between the proteins and the need of cancer cells to deal with aberrant changes in protein abundance.

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Section: Discussionmentioning

confidence: 99%

Protein Complex Organization Imposes Constraints on Proteome Dysregulation in Cancer

Senger

Schaefer

2021

Front. Bioinform.

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“…Despite the fact that GO annotation, gene expression pattern, and subcellular localization information demonstrated the accuracy of PPI networks, there could still be false positives and false negatives in PPI networks. Proteins with higher degree or betweenness centrality play crucial roles in many cellular processes [ 32 , 33 ], thus given that in this study, the virulence factors showed higher degree and betweenness centrality, indicating their functional importance. Among 195 virulence factors, the degree of 28 ranked in the top 10% of degree distribution (hubs).…”

Section: Discussionmentioning

confidence: 73%

Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis

Tang

et al. 2021

BMC Microbiol

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Background Aeromonas veronii is a bacterial pathogen in aquaculture, which produces virulence factors to enable it colonize and evade host immune defense. Given that experimental verification of virulence factors is time-consuming and laborious, few virulence factors have been characterized. Moreover, most studies have only focused on single virulence factors, resulting in biased interpretation of the pathogenesis of A. veronii. Results In this study, a PPI network at genome-wide scale for A. veronii was first constructed followed by prediction and mapping of virulence factors on the network. When topological characteristics were analyzed, the virulence factors had higher degree and betweenness centrality than other proteins in the network. In particular, the virulence factors tended to interact with each other and were enriched in two network modules. One of the modules mainly consisted of histidine kinases, response regulators, diguanylate cyclases and phosphodiesterases, which play important roles in two-component regulatory systems and the synthesis and degradation of cyclic-diGMP. Construction of the interspecies PPI network between A. veronii and its host Oreochromis niloticus revealed that the virulence factors interacted with homologous proteins in the host. Finally, the structures and interacting sites of the virulence factors during interaction with host proteins were predicted. Conclusions The findings here indicate that the virulence factors probably regulate the virulence of A. veronii by involving in signal transduction pathway and manipulate host biological processes by mimicking and binding competitively to host proteins. Our results give more insight into the pathogenesis of A. veronii and provides important information for designing targeted antibacterial drugs.

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“…PPIs provide a systems understanding of protein functionality at the cellular level (Gu et al 2011;He et al 2010;Li et al 2015). To thoroughly understand the molecular mechanism of PPIs, the identification of protein interaction sites is a crucial step.…”

Section: Discussionmentioning

confidence: 99%

AraPPISite: a database of fine-grained protein–protein interaction site annotations for Arabidopsis thaliana

Yang

Wang

et al. 2016

Plant Mol Biol

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Knowledge about protein interaction sites provides detailed information of protein-protein interactions (PPIs). To date, nearly 20,000 of PPIs from Arabidopsis thaliana have been identified. Nevertheless, the interaction site information has been largely missed by previously published PPI databases. Here, AraPPISite, a database that presents fine-grained interaction details for A. thaliana PPIs is established. First, the experimentally determined 3D structures of 27 A. thaliana PPIs are collected from the Protein Data Bank database and the predicted 3D structures of 3023 A. thaliana PPIs are modeled by using two well-established template-based docking methods. For each experimental/predicted complex structure, AraPPISite not only provides an interactive user interface for browsing interaction sites, but also lists detailed evolutionary and physicochemical properties of these sites. Second, AraPPISite assigns domain-domain interactions or domain-motif interactions to 4286 PPIs whose 3D structures cannot be modeled. In this case, users can easily query protein interaction regions at the sequence level. AraPPISite is a free and user-friendly database, which does not require user registration or any configuration on local machines. We anticipate AraPPISite can serve as a helpful database resource for the users with less experience in structural biology or protein bioinformatics to probe the details of PPIs, and thus accelerate the studies of plant genetics and functional genomics. AraPPISite is available at http://systbio.cau.edu.cn/arappisite/index.html .

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Competition-cooperation relationship networks characterize the competition and cooperation between proteins

Cited by 4 publications

References 46 publications

Protein Complex Organization Imposes Constraints on Proteome Dysregulation in Cancer

Protein Complex Organization Imposes Constraints on Proteome Dysregulation in Cancer

Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis

AraPPISite: a database of fine-grained protein–protein interaction site annotations for Arabidopsis thaliana

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