Structural characterization of flexible proteins using small-angle X-ray scattering.

By P. Bernadó, E. Mylonas, M. Petoukhov, Martin Blackledge, Dmitri I. Svergun. Journal of the American Chemical Society, 2007

1,155 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d078696f32ea5cfecbb11465c890398c83bc026a

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In Materials Chemistry

In Molecular Biology

Citations in the corpus

Phase separation in biology; functional organization of a higher order (2016, background): “, radius of gyration) of ensembles of disordered proteins [88].”
ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions (2017, methodology): “This method has been widely used to study the potential flexibility of a variety of biological systems (Bernadó et al., 2007; Tria et al., 2015).”
Structure and flexibility within proteins as identified through small angle X-ray scattering (2009, methodology): “Based on the ensemble optimization method described by Bernado et al. (2007) we have developed an algorithm which searches for the minimal ensemble (MES) of the conformations from the pool of all generated conformations.”
How Random are Intrinsically Disordered Proteins? A Small Angle Scattering Perspective (2012, background): “The program suite EOM, Ensemble Optimization Method [115], is currently the most popular due to its simple interface.”
New developments in the ATSAS program package for small-angle scattering data analysis (2012, positive): “In the ATSAS package, quantitative analysis of such systems is performed using the ensemble optimization method (EOM; Bernadó et al., 2007), which allows for a co-existence of multiple conformers in solution.”
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins (2012, background): “Intrinsically unfolded proteins, once purified, can be identified by various experimental methods [6-9].”
G3BP1 is a tunable switch that triggers phase separation to assemble stress granules (2020, neutral): “The Ranch algorithm implemented in this way generates a pool of conformations in which all IDRs are close to the self-avoiding random walk limit, i.e., there are no attractive interactions between IDRs and/or folded domains.”
FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies (2016, background): “NMR, FRET, single molecule approaches) (7) and ensemble characterization methods (8,9) enabled researchers to obtain deeper, higher-resolution views of dynamic regions in protein complexes.”
A practical guide to small angle X‐ray scattering (SAXS) of flexible and intrinsically disordered proteins (2015, methodology): “Using e.g. EOM as described above a model of flexibility is assumed in the pool generation, and the pool may or may not lead to an adequate fit to the experimental data.”
FoXS: a web server for rapid computation and fitting of SAXS profiles (2010, background): “modeling active conformation starting from non-active conformation) (11), structural characterization of flexible proteins (12,13), assembly of multi domain proteins starting from single domain structures (14), assembly of multi protein complexes (10), fold recognition and comparative modeling (15,1”