Large-scale motions in the adenylate kinase solution ensemble: Coarse-grained simulations and comparison with solution X-ray scattering

A large rapidly decreasing intensity called the `scattering tail' is generally observed at the smallest recorded angles during small-angle measurements of metallic alloys. Since this tail was interpreted as caused by a bimodal phase separation in Cu–Ni–Fe alloys and by long-wavelength concentration fluctuations in Invar alloys, these two systems were re-examined with anomalous X-ray scattering. The variation of the alloying atomic contrasts allows a discrimination between the different types of particles or defects. In neither of the two systems can the tails be interpreted as caused by large-scale concentration fluctuations. In Cu–Ni–Fe alloys, the tail is due to some kind of superficial defect (surface roughness etc.). In Invar alloys, the tail is probably due to residual impurity particles.

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Small-angle X-ray scattering constraints and local geometry like secondary structures can construct a coarse-grained protein model at amino acid residue resolution

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2012.12.091 ◽

2013 ◽

Vol 431 (1) ◽

pp. 65-69 ◽

Cited By ~ 4

Author(s):

Yasumasa Morimoto ◽

Takashi Nakagawa ◽

Masaki Kojima

Keyword(s):

Amino Acid ◽

Amino Acid Residue ◽

Small Angle ◽

Secondary Structures ◽

Coarse Grained ◽

Local Geometry ◽

X Ray ◽

X Ray Scattering ◽

Protein Model ◽

Ray Scattering

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Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments

Biophysics and Physicobiology ◽

10.2142/biophysico.16.0_377 ◽

2019 ◽

Vol 16 (0) ◽

pp. 377-390

Author(s):

Toru Ekimoto ◽

Yuichi Kokabu ◽

Tomotaka Oroguchi ◽

Mitsunori Ikeguchi

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Small Angle ◽

Coarse Grained ◽

X Ray ◽

X Ray Scattering ◽

Dynamics Simulations ◽

Coarse Grained Molecular Dynamics ◽

Ray Scattering

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Biasing RNA Coarse-Grained Folding Simulations with Small-Angle X-ray Scattering Data

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.1c00441 ◽

2021 ◽

Author(s):

Liuba Mazzanti ◽

Lina Alferkh ◽

Elisa Frezza ◽

Samuela Pasquali

Keyword(s):

Small Angle ◽

Coarse Grained ◽

Scattering Data ◽

X Ray ◽

X Ray Scattering ◽

Folding Simulations ◽

Ray Scattering

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Small-angle X-ray scattering by PVP–water mixtures

Journal of Applied Crystallography ◽

10.1107/s0021889800018689 ◽

2001 ◽

Vol 34 (1) ◽

pp. 62-64 ◽

Cited By ~ 5

Author(s):

Jan van der Elsken ◽

Wim Bras ◽

Jan Michielsen

Keyword(s):

Small Angle ◽

Large Scale ◽

Columnar Structure ◽

Water Mixture ◽

X Ray ◽

Large Scale Structures ◽

X Ray Scattering ◽

Angle Scattering ◽

Hexagonal Columnar ◽

Ray Scattering

Small-angle X-ray scattering experiments reveal the formation of large-scale structures when a 60 wt% poly(vinylpyrrolidone) (PVP)–water mixture is cooled to 260 K. The formation of these structures leads to an enhancement of continuous small-angle scattering with decreasing temperature. This is accompanied by the appearance of sharp Bragg peaks that have a very short lifetime. The scattering angles of these peaks are in accordance with a hexagonal columnar structure. It appears that such structures occasionally live long enough to undergo rotational Brownian motion.

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MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteins

Journal of Applied Crystallography ◽

10.1107/s1600576714009959 ◽

2014 ◽

Vol 47 (4) ◽

pp. 1190-1198 ◽

Cited By ~ 12

Author(s):

Stephan Niebling ◽

Alexander Björling ◽

Sebastian Westenhoff

Keyword(s):

Form Factors ◽

Coarse Graining ◽

Data Interpretation ◽

Coarse Grained ◽

Scattering Data ◽

Structural Refinement ◽

Time Resolved ◽

X Ray ◽

X Ray Scattering ◽

Ray Scattering

Time-resolved small- and wide-angle X-ray scattering (SAXS and WAXS) methods probe the structural dynamics of proteins in solution. Although technologically advanced, these methods are in many cases limited by data interpretation. The calculation of X-ray scattering profiles is computationally demanding and poses a bottleneck for all SAXS/WAXS-assisted structural refinement and, in particular, for the analysis of time-resolved data. A way of speeding up these calculations is to represent biomolecules as collections of coarse-grained scatterers. Here, such coarse-graining schemes are presented and discussed and their accuracies examined. It is demonstrated that scattering factors coincident with the popular MARTINI coarse-graining scheme produce reliable difference scattering in the range 0 < q < 0.75 Å−1. The findings are promising for future attempts at X-ray scattering data analysis, and may help to bridge the gap between time-resolved experiments and their interpretation.

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