ArticleJournal of molecular biology2008
Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
- Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications.Journal of applied crystallography · 2024Article
- Combining small angle X-ray scattering (SAXS) with protein structure predictions to characterize conformations in solution.Methods in enzymology · 2023Article
- Mechanisms of isoform-specific residue influence on GTP-bound HRas, KRas, and NRas.Biophysical journal · 2022Article
- Ferrochelatase: Mapping the Intersection of Iron and Porphyrin Metabolism in the Mitochondria.Frontiers in cell and developmental biology · 2022Review
- Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Recent Developments in Data-Assisted Modeling of Flexible Proteins.Frontiers in molecular biosciences · 2021Review
- Glycine substitution in SH3-SH2 connector of Hck tyrosine kinase causes population shift from assembled to disassembled state.Biochimica et biophysica acta. General subjects · 2020Article
- Estimating signal and noise of time-resolved X-ray solution scattering data at synchrotrons and XFELs.Journal of synchrotron radiation · 2020Article
- Neighborhood Preference of Amino Acids in Protein Structures and its Applications in Protein Structure Assessment.Scientific reports · 2020Article
- Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.Current opinion in structural biology · 2019Review
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- Formation of a new type of uranium(iv) poly-oxo cluster {UChemical science · 2018Article
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- Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Quantitative evaluation of statistical errors in small-angle X-ray scattering measurements.Journal of applied crystallography · 2017Article
- Determining Complex Structures using Docking Method with Single Particle Scattering Data.Frontiers in molecular biosciences · 2017Article
- Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods.Journal of the American Chemical Society · 2016Article
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- Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures.Journal of applied crystallography · 2016Article
- FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles.Nucleic acids research · 2016Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
A major challenge in structural biology is to determine the configuration of domains and proteins in multidomain proteins and assemblies, respectively. All available data should be considered to maximize the accuracy and precision of these models. Small-angle X-ray scattering (SAXS) efficiently provides low-resolution experimental data about the shapes of proteins and their assemblies. Thus, we integrated SAXS profiles into our software for modeling proteins and their assemblies by satisfaction of spatial restraints. Specifically, we modeled the quaternary structures of multidomain proteins with structurally defined rigid domains as well as quaternary structures of binary complexes of structurally defined rigid proteins. In addition to SAXS profiles and the component structures, we used stereochemical restraints and an atomic distance-dependent statistical potential. The scoring function is optimized by a biased Monte Carlo protocol, including quasi-Newton and simulated annealing schemes. The final prediction corresponds to the best scoring solution in the largest cluster of many independently calculated solutions. To quantify how well the quaternary structures are determined based on their SAXS profiles, we used a benchmark of 12 simulated examples as well as an experimental SAXS profile of the homotetramer D-xylose isomerase. Optimization of the SAXS-dependent scoring function generally results in accurate models if sufficiently precise approximations for the constituent rigid bodies are available; otherwise, the best scoring models can have significant errors. Thus, SAXS profiles can play a useful role in the structural characterization of proteins and assemblies if they are combined with additional data and used judiciously. Our integration of a SAXS profile into modeling by satisfaction of spatial restraints will facilitate further integration of different kinds of data for structure determination of proteins and their assemblies.
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