ArticleProceedings of the National Academy of Sciences of the United States of America2009
High-resolution protein complexes from integrating genomic information with molecular simulation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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Who cites it
78 citing papers in PubMed.
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- NucleoSeeker-precision filtering of RNA databases to curate high-quality datasets.NAR genomics and bioinformatics · 2025Article
- DiffPaSS-high-performance differentiable pairing of protein sequences using soft scores.Bioinformatics (Oxford, England) · 2024Article
- Mechanism of activation and autophosphorylation of a histidine kinase.Communications chemistry · 2024Article
- Residue coevolution and mutational landscape for OmpR and NarL: You can teach old dogs new tricks.Biophysical journal · 2024Article
- Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies.Biophysical journal · 2024Article
- pycofitness-Evaluating the fitness landscape of RNA and protein sequences.Bioinformatics (Oxford, England) · 2024Article
- Evolution shapes interaction patterns for epistasis and specific protein binding in a two-component signaling system.Communications chemistry · 2024Article
- RNA contact prediction by data efficient deep learning.Communications biology · 2023Article
- Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies.Communications medicine · 2023Review
- Design of a Protein with Improved Thermal Stability by an Evolution-Based Generative Model.Angewandte Chemie (International ed. in English) · 2022Article
- Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling.Bioinformatics (Oxford, England) · 2022Article
- Coupling a Live Cell Directed Evolution Assay with Coevolutionary Landscapes to Engineer an Improved Fluorescent Rhodopsin Chloride Sensor.ACS synthetic biology · 2022Article
- Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods.Journal of chemical theory and computation · 2022Article
- CoCoNet-boosting RNA contact prediction by convolutional neural networks.Nucleic acids research · 2021Article
- ELIHKSIR Web Server: Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators.Entropy (Basel, Switzerland) · 2021Article
- Toward Characterising the Cellular 3D-Proteome.Frontiers in bioinformatics · 2021Article
18 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
Bacteria use two-component signal transduction systems (TCS) extensively to sense and react to external stimuli. In these, a membrane-bound sensor histidine kinase (SK) autophosphorylates in response to an environmental stimulus and transfers the phosphoryl group to a transcription factor/response regulator (RR) that mediates the cellular response. The complex between these two proteins is ruled by transient interactions, which provides a challenge to experimental structure determination techniques. The functional and structural homolog of an SK/RR pair Spo0B/Spo0F, however, has been structurally resolved. Here, we describe a method capable of generating structural models of such transient protein complexes. By using existing structures of the individual proteins, our method combines bioinformatically derived contact residue information with molecular dynamics simulations. We find crystal resolution accuracy with existing crystallographic data when reconstituting the known system Spo0B/Spo0F. Using this approach, we introduce a complex structure of TM0853/TM0468 as an exemplary SK/RR TCS, consistent with all experimentally available data.
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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.