Abstract
Date hub proteins have 1 or 2 interaction interfaces but many interaction partners. This raises the question of whether all partner proteins compete for the interaction interface of the hub or if the cell carefully regulates aspects of this process? Here, we have used real-time rendering of protein interaction networks to analyse the interactions of all the 1 or 2 interface hubs of Saccharomyces cerevisiae during the cell cycle. By integrating previously determined structural and gene expression data, and visually hiding the nodes (proteins) and their edges (interactions) during their troughs of expression, we predict when interactions of hubs and their partners are likely to exist. This revealed that 20 out of all 36 one- or two- interface hubs in the yeast interactome fell within two main groups. The first was dynamic hubs with static partners, which can be considered as ‘competitive hubs’. Their interaction partners will compete for the interaction interface of the hub and the success of any interaction will be dictated by the kinetics of interaction (abundance and affinity) and subcellular localisation. The second was static hubs with dynamic partners, which we term ‘non-competitive hubs’. Regulatory mechanisms are finely tuned to lessen the presence and/or effects of competition between the interaction partners of the hub. It is possible that these regulatory processes may also be used by the cell for the regulation of other, non-cell cycle processes.
Highlights
The construction and analysis of protein-protein interaction networks has revealed that they are heterogeneous and have many interesting features
Dynamic and Static Singlish Hubs To determine if the cell has specific regulatory processes to control the interactions of date hub proteins with their partners, real time rendering [16] was used to examine all 36 singlish hubs in the yeast interactome during the cell cycle
We sought to understand whether hub proteins that have one or two interaction interfaces, or their many interaction partners, are subject to restrictions on expression to reduce competition at interaction interfaces
Summary
The construction and analysis of protein-protein interaction networks has revealed that they are heterogeneous and have many interesting features. While the absolute distinction between date and party hubs remains under debate [7,8], structural analysis of hub proteins provides a means of assessing how a protein is likely to interact with its partners and how many interactions it can participate in at once [9]. By contrast, are likely to be part of large and stable complexes, allowing the interaction with several proteins at once. These observations are supported by differences in the intrinsic disorder of hub types, whereby date hubs show high intrinsic disorder, suggesting a capacity for transient binding and flexible interfaces [11,12,13,14]
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