ArticleGeneral physiology and biophysics2009
Structure and flexibility within proteins as identified through small angle X-ray scattering.
Article in General physiology and biophysics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 269 papers.
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269 citing papers in PubMed.
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- BilboMD: a web-accessible SAXS and AlphaFold-guided modeling pipeline.Nucleic acids research · 2026Article
- Divergent Rickettsia species exhibit distinct mechanisms of actin-based motility.The Journal of cell biology · 2026Article
- A structure-based epitope tagging approach identifies vulnerable sites on the malarial P36-P52 protein complex for antibody-mediated neutralization of Plasmodium sporozoites.PLoS pathogens · 2026Article
- Integrative SAXS and AFM analysis of engineered carbohydrate-active enzyme assemblies with tunable spatial organization.Protein science : a publication of the Protein Society · 2026Article
- 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
- Structural analysis of the flexibility of the Ubl2 domain within the papain-like protease of SARS-CoV-2.Acta crystallographica. Section F, Structural biology communications · 2026Article
- Activation dynamics of a water-soluble human mu-opioid receptor.The Journal of biological chemistry · 2026Article
- Solution characterization of TraW, a regulatory protein of the F plasmid type 4 secretion system.Structural dynamics (Melville, N.Y.) · 2026Article
- EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks.Nucleic acids research · 2026Article
- PARP1-HPF1 structure and dynamics on nicked DNA suggest a mechanism for acute and localized ADP-ribosylation.Nature communications · 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
- Predicting Pose Distribution of Protein Domains Connected by Flexible Linkers Is an Unsolved Problem.Proteins · 2026Article
- Structural insights into IMP2 dimerization and RNA binding.Journal of structural biology · 2025Article
- Dynamics and structural features of the eEF1A1 and eEF1A2 paralogs.Nucleic acids research · 2025Article
- Functional Characterization of Arabidopsis α-Amylase3 (AMY3): Amylose Specificity and Structural Insights into Its Duplex Carbohydrate-Binding Module.bioRxiv : the preprint server for biology · 2025Article
- Combining simulations and experiments - a perspective on maximum entropy methods.Physical chemistry chemical physics : PCCP · 2025Review
- ALS-ENABLE: creating synergy and opportunity at the Advanced Light Source synchrotron structural biology beamlines.Journal of synchrotron radiation · 2025Article
209 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Flexibility between domains of proteins is often critical for function. These motions and proteins with large scale flexibility in general are often not readily amenable to conventional structural analysis such as X-ray crystallography, nuclear magnetic resonance spectroscopy (NMR) or electron microscopy. A common evolution of a crystallography project, once a high resolution structure has been determined, is to postulate possible sights of flexibility. Here we describe an analysis tool using relatively inexpensive small angle X-ray scattering (SAXS) measurements to identify flexibility and validate a constructed minimal ensemble of models, which represent highly populated conformations in solution. The resolution of these results is sufficient to address the questions being asked: what kinds of conformations do the domains sample in solution? In our rigid body modeling strategy BILBOMD, molecular dynamics (MD) simulations are used to explore conformational space. A common strategy is to perform the MD simulation on the domains connections at very high temperature, where the additional kinetic energy prevents the molecule from becoming trapped in a local minimum. The MD simulations provide an ensemble of molecular models from which a SAXS curve is calculated and compared to the experimental curve. A genetic algorithm is used to identify the minimal ensemble (minimal ensemble search, MES) required to best fit the experimental data. We demonstrate the use of MES in several model and in four experimental examples.
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