ArticleMolecular systems biology2008
Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size.
Article in Molecular systems biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
66 citing papers in PubMed.
- Parkinson's disease-specific α-Synuclein variants potentially drive Lewy body formation by engaging in promiscuous and non-functional interactions.Communications biology · 2026Article
- The Effect of Electron Spin-Dependent Polarizability on Protein Activity.Biomolecules · 2025Review
- The role of promiscuous molecular recognition in the evolution of RNase-based self-incompatibility in plants.Nature communications · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- A computational toolbox for the assembly yield of complex and heterogeneous structures.Nature communications · 2023Article
- Surface patches induce nonspecific binding and phase separation of antibodies.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Purifying selection enduringly acts on the sequence evolution of highly expressed proteins in Escherichia coli.G3 (Bethesda, Md.) · 2022Article
- The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database.Molecular biology and evolution · 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
- Secretory quality control constrains functional selection-associated protein structure innovation.Communications biology · 2022Article
- On the role of phase separation in the biogenesis of membraneless compartments.The EMBO journal · 2022Article
- Thermodynamics and Free Energy Landscape of BAR-Domain Dimerization from Molecular Simulations.The journal of physical chemistry. B · 2021Article
- The Missing Expression Level-Evolutionary Rate Anticorrelation in Viruses Does Not Support Protein Function as a Main Constraint on Sequence Evolution.Genome biology and evolution · 2021Article
- Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions.Journal of molecular biology · 2019Article
- The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity.Journal of molecular biology · 2019Article
- The Many Nuanced Evolutionary Consequences of Duplicated Genes.Molecular biology and evolution · 2019Article
- Stochastic protein multimerization, activity, and fitness.Physical review. E · 2018Article
- Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions.Molecules (Basel, Switzerland) · 2018Article
- Predictive regulation and human design.eLife · 2018Article
6 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Crowded intracellular environments present a challenge for proteins to form functional specific complexes while reducing non-functional interactions with promiscuous non-functional partners. Here we show how the need to minimize the waste of resources to non-functional interactions limits the proteome diversity and the average concentration of co-expressed and co-localized proteins. Using the results of high-throughput yeast 2-hybrid experiments, we estimate the characteristic strength of non-functional protein-protein interactions. By combining these data with the strengths of specific interactions, we assess the fraction of time proteins spend tied up in non-functional interactions as a function of their overall concentration. This allows us to sketch the phase diagram for baker's yeast cells using the experimentally measured concentrations and subcellular localization of their proteins. The positions of yeast compartments on the phase diagram are consistent with our hypothesis that the yeast proteome has evolved to operate closely to the upper limit of its size, whereas keeping individual protein concentrations sufficiently low to reduce non-functional interactions. These findings have implication for conceptual understanding of intracellular compartmentalization, multicellularity and differentiation.
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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.