ArticleJournal of molecular biology2018
Continuous Interdomain Orientation Distributions Reveal Components of Binding Thermodynamics.
Article in Journal of molecular biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- DL3D: visual representation of conformational ensembles of domain-linker-domain proteins.BMC bioinformatics · 2026Article
- Modeling Alternative Conformational States in CASP16.Proteins · 2026Article
- Progress and Bottlenecks for Deep Learning in Computational Structure Biology: CASP Round XVI.Proteins · 2026Article
- Predicting Pose Distribution of Protein Domains Connected by Flexible Linkers Is an Unsolved Problem.Proteins · 2026Article
- Full-Length Context Disrupts Folding of IgG-Binding Domains of Protein A.bioRxiv : the preprint server for biology · 2025Article
- Modeling Alternative Conformational States in CASP16.bioRxiv : the preprint server for biology · 2025Article
- Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology.PLoS computational biology · 2025Article
- Article
- Reweighting methods for elucidation of conformation ensembles of proteins.Current opinion in structural biology · 2022Review
- Resistor: An algorithm for predicting resistance mutations via Pareto optimization over multistate protein design and mutational signatures.Cell systems · 2022Article
- Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance.Journal of the American Chemical Society · 2021Article
- Minimization-Aware RecursiveJournal of computational biology : a journal of computational molecular cell biology · 2020Article
- Computational Analysis of Energy Landscapes Reveals Dynamic Features That Contribute to Binding of Inhibitors to CFTR-Associated Ligand.The journal of physical chemistry. B · 2019Article
- The roles of structural dynamics in the cellular functions of RNAs.Nature reviews. Molecular cell biology · 2019Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The flexibility of biological macromolecules is an important structural determinant of function. Unfortunately, the correlations between different motional modes are poorly captured by discrete ensemble representations. Here, we present new ways to both represent and visualize correlated interdomain motions. Interdomain motions are determined directly from residual dipolar couplings, represented as a continuous conformational distribution, and visualized using the disk-on-sphere representation. Using the disk-on-sphere representation, features of interdomain motions, including correlations, are intuitively visualized. The representation works especially well for multidomain systems with broad conformational distributions.This analysis also can be extended to multiple probability density modes, using a Bingham mixture model. We use this new paradigm to study the interdomain motions of staphylococcal protein A, which is a key virulence factor contributing to the pathogenicity of Staphylococcus aureus. We capture the smooth transitions between important states and demonstrate the utility of continuous distribution functions for computing the reorientational components of binding thermodynamics. Such insights allow for the dissection of the dynamic structural components of functionally important intermolecular interactions.
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