ArticleBiophysical journal2002
Addition of missing loops and domains to protein models by x-ray solution scattering.
Article in Biophysical journal, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP, TP2 and ONEG?Chemical science · 2022Article
- Current approaches to flexible loop modeling.Current research in structural biology · 2021Review
- A new clustering and nomenclature for beta turns derived from high-resolution protein structures.PLoS computational biology · 2019Article
- How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.Bioinformatics (Oxford, England) · 2017Article
- Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering.Chemical reviews · 2016Review
- Dynamic Viral Glycoprotein Machines: Approaches for Probing Transient States That Drive Membrane Fusion.Viruses · 2016Review
- Emerging applications of small angle solution scattering in structural biology.Protein science : a publication of the Protein Society · 2015Review
- Endophilin-A1 BAR domain interaction with arachidonyl CoA.Frontiers in molecular biosciences · 2014Article
- Peroxisomal proteostasis involves a Lon family protein that functions as protease and chaperone.The Journal of biological chemistry · 2012Article
- New developments in theJournal of applied crystallography · 2012Article
- How random are intrinsically disordered proteins? A small angle scattering perspective.Current protein & peptide science · 2012Review
- A combined global and local approach to elucidate spatial organization of the Mycobacterial ParB-parS partition assembly.Biochemistry · 2011Article
- Structural model of the p14/SF3b155 · branch duplex complex.RNA (New York, N.Y.) · 2011Article
- FoXS: a web server for rapid computation and fitting of SAXS profiles.Nucleic acids research · 2010Article
- Solution structure of the human signaling protein RACK1.BMC structural biology · 2010Article
- Solution structure of the major (Spy0128) and minor (Spy0125 and Spy0130) pili subunits from Streptococcus pyogenes.European biophysics journal : EBJ · 2010Article
- Portrait of an enzyme, a complete structural analysis of a multimodular {beta}-N-acetylglucosaminidase from Clostridium perfringens.The Journal of biological chemistry · 2009Article
- Structural characterization of the bradyzoite surface antigen (BSR4) from Toxoplasma gondii, a unique addition to the surface antigen glycoprotein 1-related superfamily.The Journal of biological chemistry · 2009Article
- Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies.Journal of molecular biology · 2008Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Inherent flexibility and conformational heterogeneity in proteins can often result in the absence of loops and even entire domains in structures determined by x-ray crystallographic or NMR methods. X-ray solution scattering offers the possibility of obtaining complementary information regarding the structures of these disordered protein regions. Methods are presented for adding missing loops or domains by fixing a known structure and building the unknown regions to fit the experimental scattering data obtained from the entire particle. Simulated annealing was used to minimize a scoring function containing the discrepancy between the experimental and calculated patterns and the relevant penalty terms. In low-resolution models where interface location between known and unknown parts is not available, a gas of dummy residues represents the missing domain. In high-resolution models where the interface is known, loops or domains are represented as interconnected chains (or ensembles of residues with spring forces between the C(alpha) atoms), attached to known position(s) in the available structure. Native-like folds of missing fragments can be obtained by imposing residue-specific constraints. After validation in simulated examples, the methods have been applied to add missing loops or domains to several proteins where partial structures were available.
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