ArticleProteomics2013
Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome.
Article in Proteomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- Biological and Biologically Inspired Functional Nanostructures: Insights into Structural, Optical, Thermal, and Sensing Applications.Advanced materials (Deerfield Beach, Fla.) · 2025Review
- Profiling genetic mutations in the DNA damage repair genes of oral squamous cell carcinoma patients from Pakistan.Scientific reports · 2025Article
- Computational exploration ofBiochemistry and biophysics reports · 2024Article
- Prediction of the most deleterious non-synonymous SNPs in the human IL1B gene: evidence from bioinformatics analyses.BMC genomic data · 2024Article
- The Rapid Evolution of De Novo Proteins in Structure and Complex.Genome biology and evolution · 2024Article
- Mutational Landscape and In-Silico Analysis ofACS omega · 2023Article
- Comprehensive Characterization of the Coding and Non-Coding Single Nucleotide Polymorphisms in the Tumor Protein p63 (TP63) Gene Using In Silico Tools.Biomolecules · 2021Article
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- Prediction of Deleterious Non-synonymous SNPs of Human STK11 Gene by Combining Algorithms, Molecular Docking, and Molecular Dynamics Simulation.Scientific reports · 2019Article
- Local and global anatomy of antibody-protein antigen recognition.Journal of molecular recognition : JMR · 2018Article
- Protein charge determination and implications for interactions in cell extracts.Protein science : a publication of the Protein Society · 2017Article
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 2016Review
- Structured crowding and its effects on enzyme catalysis.Topics in current chemistry · 2013Review
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Authors and funding
4 authors.
Funding
Abstract
We constructed and simulated a "minimal proteome" model using Langevin dynamics. It contains 206 essential protein types that were compiled from the literature. For comparison, we generated six proteomes with randomized concentrations. We found that the net charges and molecular weights of the proteins in the minimal genome are not random. The net charge of a protein decreases linearly with molecular weight, with small proteins being mostly positively charged and large proteins negatively charged. The protein copy numbers in the minimal genome have the tendency to maximize the number of protein-protein interactions in the network. Negatively charged proteins that tend to have larger sizes can provide a large collision cross-section allowing them to interact with other proteins; on the other hand, the smaller positively charged proteins could have higher diffusion speed and are more likely to collide with other proteins. Proteomes with random charge/mass populations form less stable clusters than those with experimental protein copy numbers. Our study suggests that "proper" populations of negatively and positively charged proteins are important for maintaining a protein-protein interaction network in a proteome. It is interesting to note that the minimal genome model based on the charge and mass of Escherichia coli may have a larger protein-protein interaction network than that based on the lower organism Mycoplasma pneumoniae.
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