ArticleProceedings of the National Academy of Sciences of the United States of America2011
Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
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- Protein Stability, Turnover Kinetics, and Abundance Constrain the Scaling of Protein Interaction Networks.bioRxiv : the preprint server for biology · 2026Article
- Parkinson's disease-specific α-Synuclein variants potentially drive Lewy body formation by engaging in promiscuous and non-functional interactions.Communications biology · 2026Article
- Genomic adaptability and virulence of Bacillus anthracis: a machine learning-based pan-genome and comparative analysis.BMC genomics · 2026Article
- Automated sparse feature selection in high-dimensional proteomics data via 1-bit compressed sensing and K-Medoids clustering.BMC bioinformatics · 2025Article
- Surface patches induce nonspecific binding and phase separation of antibodies.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Evolution of homo-oligomerization of methionine S-adenosyltransferases is replete with structure-function constrains.Protein science : a publication of the Protein Society · 2022Article
- Proteome-wide landscape of solubility limits in a bacterial cell.Scientific reports · 2022Article
- Integrating protein copy numbers with interaction networks to quantify stoichiometry in clathrin-mediated endocytosis.Scientific reports · 2022Article
- A computational exploration of resilience and evolvability of protein-protein interaction networks.Communications biology · 2021Article
- Mind the translational gap: using iPS cell models to bridge from genetic discoveries to perturbed pathways and therapeutic targets.Molecular autism · 2021Review
- Effect of Protein Structure on Evolution of Cotranslational Folding.Biophysical journal · 2020Article
- Selective Modulation of Dynamic Protein Complexes.Cell chemical biology · 2020Review
- Evolution Rapidly Optimizes Stability and Aggregation in Lattice Proteins Despite Pervasive Landscape Valleys and Mazes.Genetics · 2020Article
- Random-forest algorithm based biomarkers in predicting prognosis in the patients with hepatocellular carcinoma.Cancer cell international · 2020Article
- Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions.Journal of molecular biology · 2019Article
- Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas.Journal of molecular neuroscience : MN · 2019Article
- The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity.Journal of molecular biology · 2019Article
- Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World.Proteomes · 2018Article
- Hidden long evolutionary memory in a model biochemical network.Physical review. E · 2018Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous nonfunctional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are directly determined from its genome through biophysical properties of protein structures and binding interactions in a crowded cellular environment. The model cell includes three independent prototypical pathways, whose topologies of protein-protein interaction (PPI) subnetworks are different, but whose contributions to the cell fitness are equal. Model cells evolve through genotypic mutations and phenotypic protein copy number variations. We found a strong relationship between evolved physical-chemical properties of protein interactions and their abundances due to a "frustration" effect: Strengthening of functional interactions brings about hydrophobic interfaces, which make proteins prone to promiscuous binding. The balancing act is achieved by lowering concentrations of hub proteins while raising solubilities and abundances of functional monomers. On the basis of these principles we generated and analyzed a possible realization of the proteome-wide PPI network in yeast. In this simulation we found that high-throughput affinity capture-mass spectroscopy experiments can detect functional interactions with high fidelity only for high-abundance proteins while missing most interactions for low-abundance proteins.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.