ArticlePloS one2011
Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 97 citations in OpenAlex.
- Two-Component Systems inVeterinary sciences · 2025Review
- Crosstalk involving two-component systems inJournal of bacteriology · 2024Review
- Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies.Communications medicine · 2023Review
- Data-driven design of orthogonal protein-protein interactions.Science signaling · 2023Article
- General strategies for using amino acid sequence data to guide biochemical investigation of protein function.Biochemical Society transactions · 2022Review
- Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences.PLoS computational biology · 2022Article
- Improved prediction of protein-protein interactions using AlphaFold2.Nature communications · 2022Article
- Functional Redundancy and Specialization of the Conserved Cold Shock Proteins inMicroorganisms · 2021Article
- Inter-protein residue covariation information unravels physically interacting protein dimers.BMC bioinformatics · 2020Article
- Application of Firefly Luciferase (Luc) as a Reporter Gene for the Chemoautotrophic and Acidophilic Acidithiobacillus spp.Current microbiology · 2020Article
- A protocol to automatically calculate homo-oligomeric protein structures through the integration of evolutionary constraints and NMR ambiguous contacts.Computational and structural biotechnology journal · 2020Article
- Phylogenetic correlations can suffice to infer protein partners from sequences.PLoS computational biology · 2019Article
- A multi-scale coevolutionary approach to predict interactions between protein domains.PLoS computational biology · 2019Article
- Evolutionary couplings of amino acid residues reveal structure and function of bacterial signaling proteins.Molecular microbiology · 2019Article
- Understanding molecular mechanisms in cell signaling through natural and artificial sequence variation.Nature structural & molecular biology · 2019Review
- Response ofFrontiers in microbiology · 2019Article
- Inferring interaction partners from protein sequences using mutual information.PLoS computational biology · 2018Article
- Flexibility and constraint: Evolutionary remodeling of the sporulation initiation pathway in Firmicutes.PLoS genetics · 2018Article
- Inter-residue, inter-protein and inter-family coevolution: bridging the scales.Current opinion in structural biology · 2018Review
- Applications of sequence coevolution in membrane protein biochemistry.Biochimica et biophysica acta. Biomembranes · 2018Review
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
Abstract
Predictive understanding of the myriads of signal transduction pathways in a cell is an outstanding challenge of systems biology. Such pathways are primarily mediated by specific but transient protein-protein interactions, which are difficult to study experimentally. In this study, we dissect the specificity of protein-protein interactions governing two-component signaling (TCS) systems ubiquitously used in bacteria. Exploiting the large number of sequenced bacterial genomes and an operon structure which packages many pairs of interacting TCS proteins together, we developed a computational approach to extract a molecular interaction code capturing the preferences of a small but critical number of directly interacting residue pairs. This code is found to reflect physical interaction mechanisms, with the strongest signal coming from charged amino acids. It is used to predict the specificity of TCS interaction: Our results compare favorably to most available experimental results, including the prediction of 7 (out of 8 known) interaction partners of orphan signaling proteins in Caulobacter crescentus. Surveying among the available bacterial genomes, our results suggest 15∼25% of the TCS proteins could participate in out-of-operon "crosstalks". Additionally, we predict clusters of crosstalking candidates, expanding from the anecdotally known examples in model organisms. The tools and results presented here can be used to guide experimental studies towards a system-level understanding of two-component signaling.
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Registered trials
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.