ReviewProtein science : a publication of the Protein Society2017
The accommodation index measures the perturbation associated with insertions and deletions in coiled-coils: Application to understand signaling in histidine kinases.
Review in Protein science : a publication of the Protein Society, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed, 37 citations in OpenAlex.
- Activation mechanism of the full-length histidine kinase LvrB from pathogenic Leptospira.Nature communications · 2026Article
- Insights Into the Conformational Dynamics of the Cytoplasmic Domain of Metal-Sensing Sensor Histidine Kinase ZraS.Proteins · 2025Article
- A Designed ZnJournal of the American Chemical Society · 2025Article
- The structure of a NEMO construct engineered for screening reveals novel determinants of inhibition.Structure (London, England : 1993) · 2025Article
- Exo-chirality of the α-helix.Nature communications · 2024Article
- Atomic insights into the signaling landscape of E. coli PhoQ histidine kinase from molecular dynamics simulations.Scientific reports · 2024Article
- AlphaFold2 captures the conformational landscape of the HAMP signaling domain.Protein science : a publication of the Protein Society · 2024Article
- The coiled-coil domain of Escherichia coli FtsLB is a structurally detuned element critical for modulating its activation in bacterial cell division.The Journal of biological chemistry · 2022Article
- De novo metalloprotein design.Nature reviews. Chemistry · 2022Article
- Allosteric mechanism of signal transduction in the two-component system histidine kinase PhoQ.eLife · 2021Article
- Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity.International journal of molecular sciences · 2021Review
- Activation mechanism of a small prototypic Rec-GGDEF diguanylate cyclase.Nature communications · 2021Article
- The myosin II coiled-coil domain atomic structure in its native environment.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- A library of coiled-coil domains: from regular bundles to peculiar twists.Bioinformatics (Oxford, England) · 2021Article
- Protein design-scapes generated by microfluidic DNA assembly elucidate domain coupling in the bacterial histidine kinase CpxA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Mechanism of conditional partner selectivity in MITF/TFE family transcription factors with a conserved coiled coil stammer motif.Nucleic acids research · 2020Article
- Structural insights into the signalling mechanisms of two-component systems.Nature reviews. Microbiology · 2018Review
- Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster.Biopolymers · 2018Article
- Structure and Function of the Transmembrane Domain of NsaS, an Antibiotic Sensing Histidine Kinase in Staphylococcus aureus.Journal of the American Chemical Society · 2018Article
- Article
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 at 2 institutions in 1 country.
Funding
Abstract
Coiled-coils are essential components of many protein complexes. First discovered in structural proteins such as keratins, they have since been found to figure largely in the assembly and dynamics required for diverse functions, including membrane fusion, signal transduction and motors. Coiled-coils have a characteristic repeating seven-residue geometric and sequence motif, which is sometimes interrupted by the insertion of one or more residues. Such insertions are often highly conserved and critical to interdomain communication in signaling proteins such as bacterial histidine kinases. Here we develop the "accommodation index" as a parameter that allows automatic detection and classification of insertions based on the three dimensional structure of a protein. This method allows precise identification of the type of insertion and the "accommodation length" over which the insertion is structurally accommodated. A simple theory is presented that predicts the structural perturbations of 1, 3, 4 residue insertions as a function of the length over which the insertion is accommodated. Analysis of experimental structures is in good agreement with theory, and shows that short accommodation lengths give rise to greater perturbation of helix packing angles, changes in local helical phase, and increased structural asymmetry relative to long accommodation lengths. Cytoplasmic domains of histidine kinases in different signaling states display large changes in their accommodation lengths, which can now be seen to underlie diverse structural transitions including symmetry/asymmetry and local variations in helical phase that accompany signal transduction.
Indexed as
Identifiers
What OpenQuestion holds
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.