scholarly journals Small-angle scattering and the protein crystallographer: A relationship of ever-increasing interest

2014 ◽  
Vol 36 (1) ◽  
pp. 44-48 ◽  
Author(s):  
David J. Scott
Keyword(s):  
High Resolution ◽  
Small Angle ◽  
Intrinsically Disordered Proteins ◽  
Structural Information ◽  
Crystallographic Analysis ◽  
Small Angle Scattering ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Angle Scattering ◽  
Relationship Of

Protein crystallography is one of the great intellectual achievements of the 20th Century, and it continues to open up new vistas of research as scientists are able to visualize in exquisite detail the molecules of Life. It has become increasingly apparent, however, that not all proteins are amenable to crystallographic analysis. These include (but are not confined to) proteins with functional flexible segments, glycoproteins and intrinsically disordered proteins. There are also proteins that, although rigid and folded, refuse to crystallize as an entire full-length construct, and hence high-resolution information has to be pieced together domain by domain. It is into this space that small-angle scattering is increasingly being used as the technique of choice with regard to attainable structural information.

scholarly journals Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Utsab R. Shrestha ◽  
Jeremy C. Smith ◽  
Loukas Petridis
Keyword(s):  
Molecular Dynamics ◽  
Small Angle ◽  
Intrinsically Disordered Proteins ◽  
Chemical Shifts ◽  
Small Angle Scattering ◽  
Disordered Proteins ◽  
Scattering Data ◽  
General Applicability ◽  
Intrinsically Disordered ◽  
Angle Scattering

AbstractMolecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

scholarly journals Small-angle scattering studies of intrinsically disordered proteins and their complexes

2017 ◽  
Vol 42 ◽  
pp. 15-23 ◽  
Author(s):  
Tiago N Cordeiro ◽  
Fátima Herranz-Trillo ◽  
Annika Urbanek ◽  
Alejandro Estaña ◽  
Juan Cortés ◽  
...  
Keyword(s):  
Small Angle ◽  
Intrinsically Disordered Proteins ◽  
Small Angle Scattering ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Angle Scattering

Information retrieval from X-ray small-angle scattering with polychromatic (`white') synchrotron radiation

1983 ◽  
Vol 16 (1) ◽  
pp. 42-46 ◽  
Author(s):  
O. Glatter ◽  
P. Laggner
Keyword(s):  
Synchrotron Radiation ◽  
Small Angle ◽  
Particle Shape ◽  
Structural Information ◽  
Small Angle Scattering ◽  
Radius Of Gyration ◽  
X Ray ◽  
Angle Scattering ◽  
Slit Length ◽  
Hinge Bending

The possibilities of obtaining structural information from X-ray small-angle scattering experiments with `white' polychromatic synchrotron radiation using line collimation are investigated by numerical simulation. Theoretical scattering curves of geometrical models were smeared with the appropriate wavelength distributions and slit-length functions, afflicted by statistical noise, and then evaluated by identical methods as normally used for experimental data, as described previously [program ITP; Glatter (1977). J. Appl. Cryst. 10, 415–421]. It is shown that even for a wavelength distribution of 50% half width, the information content is not limited to the parameters derived from the central part of the scattering curves, i.e. the radius of gyration and the zero-angle intensity, but also allows qualitative information on particle shape via the distance distribution function p(r). By a `hinge-bending model' consisting of two cylinders linked together at different angles it is demonstrated that changes in the radius of gyration amounting to less than 5% can be detected and quantified, and the qualitative changes in particle shape be reproduced.

scholarly journals Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1788
Author(s):  
Vy T. Duong ◽  
Elizabeth M. Diessner ◽  
Gianmarc Grazioli ◽  
Rachel W. Martin ◽  
Carter T. Butts
Keyword(s):  
Protein Structure ◽  
Intrinsically Disordered Proteins ◽  
Dynamic Models ◽  
Structural Information ◽  
Coarse Graining ◽  
Molecular Structures ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Scalable Network ◽  
Atomic Coordinates

Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a particularly useful way of obtaining highly compressed representations of molecular structures, and simulations operating via such representations can achieve substantial computational savings. A drawback of coarse-graining, however, is the loss of atomistic detail—an effect that is especially acute for topological representations such as protein structure networks (PSNs). Here, we introduce an approach based on a combination of machine learning and physically-guided refinement for inferring atomic coordinates from PSNs. This “neural upscaling” procedure exploits the constraints implied by PSNs on possible configurations, as well as differences in the likelihood of observing different configurations with the same PSN. Using a 1 μs atomistic molecular dynamics trajectory of Aβ1–40, we show that neural upscaling is able to effectively recapitulate detailed structural information for intrinsically disordered proteins, being particularly successful in recovering features such as transient secondary structure. These results suggest that scalable network-based models for protein structure and dynamics may be used in settings where atomistic detail is desired, with upscaling employed to impute atomic coordinates from PSNs.

scholarly journals Characterizing Intrinsically Disordered Proteins by Small-Angle Neutron Scattering

2011 ◽  
Vol 100 (3) ◽  
pp. 63a
Author(s):  
Christopher B. Stanley ◽  
Laura Grese ◽  
Erica Rowe ◽  
Hugh O'Neill ◽  
Valerie Berthelier
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Intrinsically Disordered

Small-angle scattering gives direct structural information about a membrane protein inside a lipid environment

2014 ◽  
Vol 70 (2) ◽  
pp. 371-383 ◽  
Author(s):  
Søren A. R. Kynde ◽  
Nicholas Skar-Gislinge ◽  
Martin Cramer Pedersen ◽  
Søren Roi Midtgaard ◽  
Jens Baek Simonsen ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Small Angle ◽  
Structural Information ◽  
Protein Localization ◽  
Hybrid Approach ◽  
Small Angle Scattering ◽  
Phospholipid Bilayer ◽  
Scattering Data ◽  
Angle Scattering ◽  
Lipid Environment

Monomeric bacteriorhodopsin (bR) reconstituted into POPC/POPG-containing nanodiscs was investigated by combined small-angle neutron and X-ray scattering. A novel hybrid approach to small-angle scattering data analysis was developed. In combination, these provided direct structural insight into membrane-protein localization in the nanodisc and into the protein–lipid interactions. It was found that bR is laterally decentred in the plane of the disc and is slightly tilted in the phospholipid bilayer. The thickness of the bilayer is reduced in response to the incorporation of bR. The observed tilt of bR is in good accordance with previously performed theoretical predictions and computer simulations based on the bR crystal structure. The result is a significant and essential step on the way to developing a general small-angle scattering-based method for determining the low-resolution structures of membrane proteins in physiologically relevant environments.

scholarly journals KWS-1: Small-angle scattering diffractometer

2015 ◽  
Vol 1 ◽  
Author(s):  
Henrich Frielinghaus ◽  
Artem Feoktystov ◽  
Ida Berts ◽  
Gaetano Mangiapia
Keyword(s):  
High Resolution ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Small Angle Scattering ◽  
Angle Scattering

The KWS-1, which is operated by JCNS, Forschungszentrum Jülich, is a small-angle neutron scattering diffractometer dedicated to high resolution measurements.

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