Structure and flexibility within proteins as identified through small angle X-ray scattering

By Martin Pelikan, Greg L. Hura, M. Hammel. 2009

421 citations recorded by the source corpus.

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.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

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Citations in the corpus

Principles of protein structural ensemble determination. (2017, methodology): “These approaches include the ‘ensemble optimization method’ (EOM) [45], the ‘selection tool for ensemble representations of intrinsically disordered states’ (ASTEROIDS) [46], the ‘sparse ensemble selection’ (SES) method [47], the ‘sample and select’ (SAS) method [48], the ‘maximum occurrence’ (MaxOc”
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”
Small‐angle scattering for structural biology—Expanding the frontier while avoiding the pitfalls (2010, methodology): “If a system cannot be adequately described by simple rigid-body modeling, it is possible to consider conformational flexibility using an ensemble model with the ensemble optimization method63 or BIBLIOMOD.64 Because of the very high parameterization of ensemble modeling, extreme care must be taken t”
How Random are Intrinsically Disordered Proteins? A Small Angle Scattering Perspective (2012, background): “php) aims to determine the minimal ensemble that best fits the data [27].”
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop (2015, neutral): “Second, a model can be multi-state, specifying multiple discrete states of the system required to explain the input information (each state may differ in structure, composition, or both) (Molnar et al., 2014; Pelikan et al., 2009).”
Computational design of trimeric influenza neutralizing proteins targeting the hemagglutinin receptor binding site (2017, methodology): “Digestion was instantly quenched by mixing with 6 μL of 2× Laemmli Sample Buffer (Bio-Rad) and incubating it for 2 min at 95°C. Samples were loaded onto a 12% NuPage Bis-Tris gel (Life Technologies, Carlsbad, CA) and run 1× MES buffer (50 mM MES, 50 mM Tris Base, 0.1% SDS, 1 mM EDTA, pH 7.3).”
A practical guide to small angle X‐ray scattering (SAXS) of flexible and intrinsically disordered proteins (2015, methodology): “For SAXS applications several approaches have been developed to characterize protein mobility: The Ensemble Optimization Method (EOM) [41,42], the Minimal Ensemble Search (MES) [43], Basis-Set Supported SAXS (BSS-SAXS) [44], the Ensemble Refinement of SAXS (EROS) [45].”