Tertiary Structure of α-1 Peptide of Globin Hydrolysates by the Small-Angle Solution X-ray Scattering Method

Clays and soils produce strong small-angle X-ray scattering (SAXS) because they contain large numbers of nanoparticles, namely allophane and ferrihydrite. These nanoparticles are amorphous and have approximately spherical shape with a size of around 3–10 nm. The weight ratios of these nanoparticles will affect the properties of the clays and soils. However, the nanoparticles in clays and soils are not generally quantified and are sometimes ignored because there is no standard method to quantify them. This paper describes a method to quantify nanoparticles in clays and soils with SAXS. This is achieved by deriving normalized SAXS intensities from unit weight of the sample, which are not affected by absorption. By integrating the normalized SAXS intensities over the reciprocal space, one obtains a value that is proportional to the weight ratio of the nanoparticles, proportional to the square of the difference of density between the nanoparticles and the liquid surrounding the nanoparticles, and inversely proportional to the density of the nanoparticles. If the density of the nanoparticles is known, the weight ratio of the nanoparticles can be calculated from the SAXS intensities. The density of nanoparticles was estimated from the chemical composition of the sample. Nanoparticles in colloidal silica, silica gels, mixtures of silica gel and α-aluminium oxide, and synthetic clays have been quantified with the integral SAXS method. The results show that the errors of the weight ratios of nanoparticles are around 25% of the weight ratio. It is also shown that some natural clays contain large fractions of nanoparticles; montmorillonite clay from the Mikawa deposit, pyrophillite clay from the Shokozan deposit and kaolinite clay from the Kanpaku deposit contain 25 (7), 10 (2) and 19 (5) wt% nanoparticles, respectively, where errors are shown in parentheses.

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Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept

Scientific Reports ◽

10.1038/srep12085 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 19

Author(s):

Nicholas Allec ◽

Mina Choi ◽

Nikhil Yesupriya ◽

Brian Szychowski ◽

Michael R. White ◽

...

Keyword(s):

Molecular Interactions ◽

Small Angle ◽

Scattering Method ◽

Proof Of Concept ◽

X Ray ◽

X Ray Scattering ◽

Ray Scattering

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Morphological study of conductive polyaniline/polyimide blends. I. Determination of compatibility by small-angle X-ray scattering method

Polymer ◽

10.1016/s0032-3861(01)00244-0 ◽

2001 ◽

Vol 42 (17) ◽

pp. 7449-7454 ◽

Cited By ~ 16

Author(s):

Moon Gyu Han ◽

Seung Soon Im

Keyword(s):

Small Angle ◽

Morphological Study ◽

Scattering Method ◽

X Ray ◽

X Ray Scattering ◽

Conductive Polyaniline ◽

Ray Scattering

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Determination of protein crystallization kinetics by a through-flow small-angle X-ray scattering method

Chemical Engineering Research and Design ◽

10.1016/j.cherd.2018.11.030 ◽

2019 ◽

Vol 141 ◽

pp. 580-591 ◽

Cited By ~ 1

Author(s):

Izabela Poplewska ◽

Andrzej Łyskowski ◽

Michał Kołodziej ◽

Piotr Szałański ◽

Wojciech Piątkowski ◽

...

Keyword(s):

Crystallization Kinetics ◽

Small Angle ◽

Protein Crystallization ◽

Scattering Method ◽

X Ray ◽

X Ray Scattering ◽

Through Flow ◽

Ray Scattering

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SAXSDom: Modeling multi-domain protein structures using small-angle X-ray scattering data

10.1101/559617 ◽

2019 ◽

Author(s):

Jie Hou ◽

Badri Adhikari ◽

John J. Tanner ◽

Jianlin Cheng

Keyword(s):

Homology Modeling ◽

Small Angle ◽

Tertiary Structure ◽

Protein Structures ◽

Scattering Data ◽

Multidomain Proteins ◽

X Ray ◽

X Ray Scattering ◽

Domain Protein ◽

Ray Scattering

AbstractMany proteins are composed of several domains that pack together into a complex tertiary structure. Some multidomain proteins can be challenging for protein structure modeling, particularly those for which templates can be found for the domains but not for the entire sequence. In such cases, homology modeling can generate high quality models of the domains but not for the assembled protein. Small-angle X-ray scattering (SAXS) reports on the solution structural properties of proteins and has the potential for guiding homology modeling of multidomain proteins. In this work, we describe a novel multi-domain protein assembly modeling method, SAXSDom, that integrates experimental knowledge from SAXS profiles with probabilistic Input-Output Hidden Markov model (IOHMM). Four scoring functions to account for the energetic contribution of SAXS restraints for domain assembly were developed and tested. The method was evaluated on multi-domain proteins from two public datasets. Based on the results, the accuracy of domain assembly was improved for 40 out of 46 CASP multi-domain proteins in terms of RMSD and TM-score when SAXS information was used. Our method also achieved higher accuracy for at least 45 out of 73 multi-domain proteins according to RMSD and TM-score metrics in the AIDA dataset. The results demonstrate that SAXS data can provide useful information to improve the accuracy of domain-domain assembly. The source code and tool packages are available at http://github.com/multicom-toolbox/SAXSDom.

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