ArticleIUCrJ2015
Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering.
Article in IUCrJ, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 355 papers.
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Who cites it
355 citing papers in PubMed.
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- The Rho guanine-nucleotide exchange factor P-Rex2 exhibits structural and regulatory features distinct from the related RhoGEF P-Rex1.The Journal of biological chemistry · 2026Article
- Use of biomolecular emulator for characterizing flexible proteins by small-angle x-ray scattering.Protein science : a publication of the Protein Society · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
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- Structural characterization of OsPDIL2-3, a rice protein disulfide isomerase involved in prolamin accumulation.The Biochemical journal · 2026Article
- Time-Resolved SAXS Reveals Distinct Millisecond Metal-Induced Conformational Dynamics of Monomeric α-Synuclein.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
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- Coiled-coil homo-oligomerization and disaggregase Hsp104 act in parallel to stabilize orphan septins.bioRxiv : the preprint server for biology · 2026Article
- The role of linker length and composition in actin binding and bundling by palladin.The Biochemical journal · 2026Article
- P-Rex2 exhibits unique structural features and regulatory mechanisms distinct from the closely related RhoGEF P-Rex1.bioRxiv : the preprint server for biology · 2026Article
- Disordered N-termini enhance the thermostability of SGNH-hydrolase family polyesterases.Protein science : a publication of the Protein Society · 2026Article
- Structural and biophysical insights into RomR, MglB, and MglC interactions involved in regulating cell polarity in Myxococcus xanthus.The Journal of biological chemistry · 2025Article
- Sequence-encoded tubular architectures in disordered spider silk proteins revealed by multiscale simulations and NMR.PNAS nexus · 2025Article
- Dissecting the Mechanisms Underlying Substrate Recognition and Functional Regulation of O-GlcNAc Cycling Enzymes.ACS chemical biology · 2025Review
- Spermine modulation of Alzheimer's Tau and Parkinson's α-synuclein: implications for biomolecular condensation and neurodegeneration.Nature communications · 2025Article
- The Role of Linker Length and Composition in Actin Binding and Bundling by Palladin.bioRxiv : the preprint server for biology · 2025Article
295 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Dynamic ensembles of macromolecules mediate essential processes in biology. Understanding the mechanisms driving the function and molecular interactions of 'unstructured' and flexible molecules requires alternative approaches to those traditionally employed in structural biology. Small-angle X-ray scattering (SAXS) is an established method for structural characterization of biological macromolecules in solution, and is directly applicable to the study of flexible systems such as intrinsically disordered proteins and multi-domain proteins with unstructured regions. The Ensemble Optimization Method (EOM) [Bernadó et al. (2007 ▶). J. Am. Chem. Soc. 129, 5656-5664] was the first approach introducing the concept of ensemble fitting of the SAXS data from flexible systems. In this approach, a large pool of macromolecules covering the available conformational space is generated and a sub-ensemble of conformers coexisting in solution is selected guided by the fit to the experimental SAXS data. This paper presents a series of new developments and advancements to the method, including significantly enhanced functionality and also quantitative metrics for the characterization of the results. Building on the original concept of ensemble optimization, the algorithms for pool generation have been redesigned to allow for the construction of partially or completely symmetric oligomeric models, and the selection procedure was improved to refine the size of the ensemble. Quantitative measures of the flexibility of the system studied, based on the characteristic integral parameters of the selected ensemble, are introduced. These improvements are implemented in the new EOM version 2.0, and the capabilities as well as inherent limitations of the ensemble approach in SAXS, and of EOM 2.0 in particular, are discussed.
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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.