Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Open-Bundle Structure as the Unfolding Intermediate of Cytochrome c' Revealed by Small Angle Neutron Scattering.

ABSTRACT: The dynamic structure changes, including the unfolding, dimerization, and transition from the compact to the open-bundle unfolding intermediate structure of Cyt c', were detected by a small-angle neutron scattering experiment (SANS). The structure of Cyt c' was changed into an unstructured random coil at pD = 1.7 (R_g = 25 Å for the Cyt c' monomer). The four-α-helix bundle structure of Cyt c' at neutral pH was transitioned to an open-bundle structure (at pD ~13), which is given by a numerical partial scattering function analysis as a joint-clubs model consisting of four clubs (α-helices) connected by short loops. The compactly folded structure of Cyt c' (radius of gyration, R_g = 18 Å for the Cyt c' dimer) at neutral or mildly alkaline pD transited to a remarkably larger open-bundle structure at pD ~13 (R_g = 25 Å for the Cyt c' monomer). The open-bundle structure was also supported by ab initio modeling.

SUBMITTER: Yamaguchi T

PROVIDER: S-EPMC8774185 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Microfluidic devices for small-angle neutron scattering.

Project description:A comparative examination is presented of materials and approaches for the fabrication of microfluidic devices for small-angle neutron scattering (SANS). Representative inorganic glasses, metals, and polymer materials and devices are evaluated under typical SANS configurations. Performance criteria include neutron absorption, scattering background and activation, as well as spatial resolution, chemical compatibility and pressure resistance, and also cost, durability and manufacturability. Closed-face polymer photolithography between boron-free glass (or quartz) plates emerges as an attractive approach for rapidly prototyped microfluidic SANS devices, with transmissions up to ∼98% and background similar to a standard liquid cell (I ≃ 10-3 cm-1). For applications requiring higher durability and/or chemical, thermal and pressure resistance, sintered or etched boron-free glass and silicon devices offer superior performance, at the expense of various fabrication requirements, and are increasingly available commercially.

| S-EPMC5988002 | biostudies-literature

Looking into Limoncello: The Structure of the Italian Liquor Revealed by Small-Angle Neutron Scattering.

Project description:Limoncello, the Italian liquor based on lemon essential oils, is becoming increasingly popular around the world. This digestive is not only an iconic representative of Italian food culture, but it is also a complex colloidal system, made of essential oils, ethanol, sucrose, and water. Smell, aroma, taste, and appearance of Limoncello do, of course, depend on the components, in particular on the peculiar essential oil mixture. Accordingly, several studies are available in the literature investigating the composition of various Limoncellos. However, the microscopic structure plays an equally important role when it comes to the sensory properties of food and beverages. In this work, small-angle neutron scattering was used to probe the microscopic structure of Limoncello, revealing the presence of spontaneously formed 100 nm-sized droplets over a large range of composition and temperature. The results are not limited to this famous drink but can be extended to the rapidly developing formulations based on water-insoluble oils, water, and alcohols.

| S-EPMC6644077 | biostudies-literature

Kinetic asymmetry of subunit exchange of homooligomeric protein as revealed by deuteration-assisted small-angle neutron scattering.

Project description:We developed a novel, to our knowledge, technique for real-time monitoring of subunit exchange in homooligomeric proteins, using deuteration-assisted small-angle neutron scattering (SANS), and applied it to the tetradecamer of the proteasome α7 subunit. Isotopically normal and deuterated tetradecamers exhibited identical SANS profiles in 81% D(2)O solution. After mixing these solutions, the isotope sensitive SANS intensity in the low-q region gradually decreased, indicating subunit exchange, whereas the small-angle x-ray scattering profile remained unchanged confirming the structural integrity of the tetradecamer particles during the exchange. Kinetic analysis of zero-angle scattering intensity indicated that 1), only two of the 14 subunits were exchanged in each tetradecamer and 2), the exchange process involves at least two steps. This study underscores the usefulness of deuteration-assisted SANS, which can provide quantitative information not only on the molecular sizes and shapes of homooligomeric proteins, but also on their kinetic properties.

| S-EPMC3192978 | biostudies-literature

Confinement Facilitated Protein Stabilization As Investigated by Small-Angle Neutron Scattering.

Project description:While mesoporous silicas have been shown to be a compelling candidate for drug delivery and the implementation of biotechnological applications requiring protein confinement and immobilization, the understanding of protein behavior upon physical adsorption into silica pores is limited. Many indirect methods are available to assess general adsorbed protein stability, such as Fourier-transform infrared spectroscopy and activity assays. However, the limitation of these methods is that spatial protein arrangement within the pores cannot be assessed. Mesoporous silicas pose a distinct challenge to direct methods, such as transmission electron microscopy, which lacks the contrast and resolution required to adequately observe immobilized protein structure, and nuclear magnetic resonance, which is computationally intensive and requires knowledge of the primary structure a priori. Small-angle neutron scattering can surmount these limitations and observe spatial protein arrangement within pores. Hereby, we observe the stabilization of fluid-like protein arrangement, facilitated by geometry-dependent crowding effects in cylindrical pores of ordered mesoporous silica, SBA-15. Stabilization is induced from a fluid-like structure factor, which is observed for samples at maximum protein loading in SBA-15 with pore diameters of 6.4 and 8.1 nm. Application of this effect for prevention of irreversible aggregation in high concentration environments is proposed.

| S-EPMC6187370 | biostudies-literature

Grazing-incidence small-angle neutron scattering from structures below an interface.

Project description:Changes of scattering are observed as the grazing angle of incidence of an incoming beam increases and probes different depths in samples. A model has been developed to describe the observed intensity in grazing-incidence small-angle neutron scattering (GISANS) experiments. This includes the significant effects of instrument resolution, the sample transmission, which depends on both absorption and scattering, and the sample structure. The calculations are tested with self-organized structures of two colloidal samples with different size particles that were measured on two different instruments. The model allows calculations for various instruments with defined resolution and can be used to design future improved experiments. The possibilities and limits of GISANS for different studies are discussed using the model calculations.

| S-EPMC5541351 | biostudies-literature

Sub-millisecond time-resolved small-angle neutron scattering measurements at NIST.

Project description:Instrumentation for time-resolved small-angle neutron scattering measurements with sub-millisecond time resolution, based on Gähler's TISANE (time-involved small-angle neutron experiments) concept, is in operation at NIST's Center for Neutron Research. This implementation of the technique includes novel electronics for synchronizing the neutron pulses from high-speed counter-rotating choppers with a periodic stimulus applied to a sample. Instrumentation details are described along with measurements demonstrating the utility of the technique for elucidating the reorientation dynamics of anisometric magnetic particles.

| S-EPMC7312138 | biostudies-literature

Small-angle neutron scattering modeling of spin disorder in nanoparticles.

Project description:Magnetic small-angle neutron scattering (SANS) is a powerful technique for investigating magnetic nanoparticle assemblies in nonmagnetic matrices. For such microstructures, the standard theory of magnetic SANS assumes uniformly magnetized nanoparticles (macrospin model). However, there exist many experimental and theoretical studies which suggest that this assumption is violated: deviations from ellipsoidal particle shape, crystalline defects, or the interplay between various magnetic interactions (exchange, magnetic anisotropy, magnetostatics, external field) may lead to nonuniform spin structures. Therefore, a theoretical framework of magnetic SANS of nanoparticles needs to be developed. Here, we report numerical micromagnetic simulations of the static spin structure and related unpolarized magnetic SANS of a single cobalt nanorod. While in the saturated state the magnetic SANS cross section is (as expected) determined by the particle form factor, significant deviations appear for nonsaturated states; specifically, at remanence, domain-wall and vortex states emerge which result in a magnetic SANS signal that is composed of all three magnetization Fourier components, giving rise to a complex angular anisotropy on a two-dimensional detector. The strength of the micromagnetic simulation methodology is the possibility to decompose the cross section into the individual Fourier components, which allows one to draw important conclusions regarding the fundamentals of magnetic SANS.

| S-EPMC5638870 | biostudies-other

Bundling of cellulose microfibrils in native and polyethylene glycol-containing wood cell walls revealed by small-angle neutron scattering.

Project description:Wood and other plant-based resources provide abundant, renewable raw materials for a variety of applications. Nevertheless, their utilization would greatly benefit from more efficient and accurate methods to characterize the detailed nanoscale architecture of plant cell walls. Non-invasive techniques such as neutron and X-ray scattering hold a promise for elucidating the hierarchical cell wall structure and any changes in its morphology, but their use is hindered by challenges in interpreting the experimental data. We used small-angle neutron scattering in combination with contrast variation by poly(ethylene glycol) (PEG) to identify the scattering contribution from cellulose microfibril bundles in native wood cell walls. Using this method, mean diameters for the microfibril bundles from 12 to 19 nm were determined, without the necessity of cutting, drying or freezing the cell wall. The packing distance of the individual microfibrils inside the bundles can be obtained from the same data. This finding opens up possibilities for further utilization of small-angle scattering in characterizing the plant cell wall nanostructure and its response to chemical, physical and biological modifications or even in situ treatments. Moreover, our results give new insights into the interaction between PEG and the wood nanostructure, which may be helpful for preservation of archaeological woods.

| S-EPMC7705696 | biostudies-literature

Characterization of colloidal structures during intestinal lipolysis using small-angle neutron scattering.

Project description:Bile micelles are thought to mediate intestinal absorption, in part by providing a phase into which compounds can partition. Solubilizing capacity of bile micelles is enhanced during the digestion of fat rich food. We hypothesized that the intestinal digestion of triglycerides causes an increase in volume of micelles that can be quantitatively monitored over the course of digestion using small-angle neutron scattering (SANS), and that SANS can enable evaluation of the contribution of each of the components present during digestion to the size of micelles.SANS was used to characterize the size and shape of micelles present prior to and during the in vitro simulated intestinal digestion of a model food-associated lipid, triolein.Pre-lipolysis mixtures of a bile salt and phospholipid simulating bile concentrations in fed conditions were organized in micelles with an average volume of 40 nm3. During lipolysis, the micelle volume increased 2.5-fold over a 2-h digestion period due to growth in one direction as a result of insertion of monoglycerides and fatty acids. These efforts represent a basis for quantitative mechanistic understanding of changes in solubilizing capacity of the intestinal milieu upon ingestion of a fat-rich meal.

| S-EPMC5627765 | biostudies-literature

Solution Structure of an Intramembrane Aspartyl Protease via Small Angle Neutron Scattering.

Project description:Intramembrane aspartyl proteases (IAPs) comprise one of four families of integral membrane proteases that hydrolyze substrates within the hydrophobic lipid bilayer. IAPs include signal peptide peptidase, which processes remnant signal peptides from nascent polypeptides in the endoplasmic reticulum, and presenilin, the catalytic component of the ?-secretase complex that processes Notch and amyloid precursor protein. Despite their broad biomedical reach, basic structure-function relationships of IAPs remain active areas of research. Characterization of membrane-bound proteins is notoriously challenging due to their inherently hydrophobic character. For IAPs, oligomerization state in solution is one outstanding question, with previous proposals for monomer, dimer, tetramer, and octamer. Here we used small angle neutron scattering (SANS) to characterize n-dodecyl-?-D-maltopyranoside (DDM) detergent solutions containing and absent a microbial IAP ortholog. A unique feature of SANS is the ability to modulate the solvent composition to mask all but the enzyme of interest. The signal from the IAP was enhanced by deuteration and, uniquely, scattering from DDM and buffers were matched by the use of both tail-deuterated DDM and D2O. The radius of gyration calculated for IAP and the corresponding ab initio consensus model are consistent with a monomer. The model is slightly smaller than the crystallographic IAP monomer, suggesting a more compact protein in solution compared with the crystal lattice. Our study provides direct insight into the oligomeric state of purified IAP in surfactant solution, and demonstrates the utility of fully contrast-matching the detergent in SANS to characterize other intramembrane proteases and their membrane-bound substrates.

| S-EPMC5985038 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data