ArticleNature methods2013
Automated identification of functional dynamic contact networks from X-ray crystallography.
Article in Nature methods, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed.
- Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.Proteins · 2026Article
- Putrescine-bound structure and multi-temperature crystallography provide new insights into ligand binding and conformational heterogeneity in spermidine synthase.Structural dynamics (Melville, N.Y.) · 2026Article
- Allosteric network of dynamic coupling within BAP1-UCH revealed by methyl NMR.Nature communications · 2026Article
- Unfreezing structural biology for drug discovery.Nature chemical biology · 2026Review
- Hydrogen-deuterium exchange reveals catalytically linked protein flexibility in myoglobin-mediated intramolecular C(spProtein science : a publication of the Protein Society · 2026Article
- Exploring antibiotic resistance in diverse homologs of the dihydrofolate reductase protein family through broad mutational scanning.Science advances · 2025Article
- Mapping allosteric rewiring in related protein structures from collections of crystallographic multiconformer models.bioRxiv : the preprint server for biology · 2025Article
- Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Alternate conformations found in protein structures implies biological functions: A case study using cyclophilin A.Current research in structural biology · 2024Article
- High-resolution double vision of the allosteric phosphatase PTP1B.Acta crystallographica. Section F, Structural biology communications · 2024Article
- Allosteric regulatory control in dihydrofolate reductase is revealed by dynamic asymmetry.Protein science : a publication of the Protein Society · 2023Article
- Disease mutations and phosphorylation alter the allosteric pathways involved in autoinhibition of protein phosphatase 2A.The Journal of chemical physics · 2023Article
- Is Posttranslational Folding More Efficient Than Refolding from a Denatured State: A Computational Study.The journal of physical chemistry. B · 2023Article
- Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics.Annual review of biophysics · 2023Review
- Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Interpreting macromolecular diffraction through simulation.Methods in enzymology · 2023Article
- Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization.Acta crystallographica. Section D, Structural biology · 2023Article
- Room-temperature serial synchrotron crystallography of the human phosphatase PTP1B.Acta crystallographica. Section F, Structural biology communications · 2023Article
- Modeling Ensembles of Enzyme Reaction Pathways with Hi-MSM Reveals the Importance of Accounting for Pathway Diversity.The journal of physical chemistry. B · 2022Article
- Functional roles of enzyme dynamics in accelerating active site chemistry: Emerging techniques and changing concepts.Current opinion in structural biology · 2022Review
28 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
Abstract
Protein function often depends on the exchange between conformational substates. Allosteric ligand binding or distal mutations can stabilize specific active-site conformations and consequently alter protein function. Observing alternative conformations at low levels of electron density, in addition to comparison of independently determined X-ray crystal structures, can provide mechanistic insights into conformational dynamics. Here we report a new algorithm, CONTACT, that identifies contact networks of conformationally heterogeneous residues directly from high-resolution X-ray crystallography data. Contact networks determined for Escherichia coli dihydrofolate reductase (ecDHFR) predict the observed long-range pattern of NMR chemical shift perturbations of an allosteric mutation. A comparison of contact networks in wild-type and mutant ecDHFR suggests that mutations that alter optimized contact networks of coordinated motions can impair catalytic function. CONTACT-guided mutagenesis can exploit the structure-dynamics-function relationship in protein engineering and design.
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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.