Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Local Crystalline Structure in an Amorphous Protein Dense Phase.

ABSTRACT: Proteins exhibit a variety of dense phases ranging from gels, aggregates, and precipitates to crystalline phases and dense liquids. Although the structure of the crystalline phase is known in atomistic detail, little attention has been paid to noncrystalline protein dense phases, and in many cases the structures of these phases are assumed to be fully amorphous. In this work, we used small-angle neutron scattering, electron microscopy, and electron tomography to measure the structure of ovalbumin precipitate particles salted out with ammonium sulfate. We found that the ovalbumin phase-separates into core-shell particles with a core radius of ?2 ?m and shell thickness of ?0.5 ?m. Within this shell region, nanostructures comprised of crystallites of ovalbumin self-assemble into a well-defined bicontinuous network with branches ?12 nm thick. These results demonstrate that the protein gel is comprised in part of nanocrystalline protein.

SUBMITTER: Greene DG

PROVIDER: S-EPMC4623890 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Local Crystalline Structure in an Amorphous Protein Dense Phase.

Greene Daniel G DG Modla Shannon S Wagner Norman J NJ Sandler Stanley I SI Lenhoff Abraham M AM

Biophysical journal 20151001 8

Proteins exhibit a variety of dense phases ranging from gels, aggregates, and precipitates to crystalline phases and dense liquids. Although the structure of the crystalline phase is known in atomistic detail, little attention has been paid to noncrystalline protein dense phases, and in many cases the structures of these phases are assumed to be fully amorphous. In this work, we used small-angle neutron scattering, electron microscopy, and electron tomography to measure the structure of ovalbumi ...[more]

PMID: 26488663

Similar Datasets

Viscous friction between crystalline and amorphous phase of dragline silk.

Project description:The hierarchical structure of spider dragline silk is composed of two major constituents, the amorphous phase and crystalline units, and its mechanical response has been attributed to these prime constituents. Silk mechanics, however, might also be influenced by the resistance against sliding of these two phases relative to each other under load. We here used atomistic molecular dynamics (MD) simulations to obtain friction forces for the relative sliding of the amorphous phase and crystalline units of Araneus diadematus spider silk. We computed the coefficient of viscosity of this interface to be in the order of 10(2) Ns/m(2) by extrapolating our simulation data to the viscous limit. Interestingly, this value is two orders of magnitude smaller than the coefficient of viscosity within the amorphous phase. This suggests that sliding along a planar and homogeneous surface of straight polyalanine chains is much less hindered than within entangled disordered chains. Finally, in a simple finite element model, which is based on parameters determined from MD simulations including the newly deduced coefficient of viscosity, we assessed the frictional behavior between these two components for the experimental range of relative pulling velocities. We found that a perfectly relative horizontal motion has no significant resistance against sliding, however, slightly inclined loading causes measurable resistance. Our analysis paves the way towards a finite element model of silk fibers in which crystalline units can slide, move and rearrange themselves in the fiber during loading.

| S-EPMC4132047 | biostudies-literature

Topochemical conversion of a dense metal-organic framework from a crystalline insulator to an amorphous semiconductor.

Project description:The topochemical conversion of a dense, insulating metal-organic framework (MOF) into a semiconducting amorphous MOF is described. Treatment of single crystals of copper(i) chloride trithiocyanurate, CuICl(ttcH3) (ttcH3 = trithiocyanuric acid), 1, in aqueous ammonia solution yields monoliths of amorphous CuI1.8(ttc)0.6(ttcH3)0.4, 3. The treatment changes the transparent orange crystals of 1 into shiny black monoliths of 3 with retention of morphology, and moreover increases the electrical conductivity from insulating to semiconducting (conductivity of 3 ranges from 4.2 × 10-11 S cm-1 at 20 °C to 7.6 × 10-9 S cm-1 at 140 °C; activation energy = 0.59 eV; optical band gap = 0.6 eV). The structure and properties of the amorphous conductor are fully characterized by AC impedance spectroscopy, X-ray photoelectron spectroscopy, X-ray pair distribution function analysis, infrared spectroscopy, diffuse reflectance spectroscopy, electron spin resonance spectroscopy, elemental analysis, thermogravimetric analysis, and theoretical calculations.

| S-EPMC5811114 | biostudies-literature

Ductile crystalline-amorphous nanolaminates.

Project description:It is known that the room-temperature plastic deformation of bulk metallic glasses is compromised by strain softening and shear localization, resulting in near-zero tensile ductility. The incorporation of metallic glasses into engineering materials, therefore, is often accompanied by complete brittleness or an apparent loss of useful tensile ductility. Here we report the observation of an exceptional tensile ductility in crystalline copper/copper-zirconium glass nanolaminates. These nanocrystalline-amorphous nanolaminates exhibit a high flow stress of 1.09 +/- 0.02 GPa, a nearly elastic-perfectly plastic behavior without necking, and a tensile elongation to failure of 13.8 +/- 1.7%, which is six to eight times higher than that typically observed in conventional crystalline-crystalline nanolaminates (<2%) and most other nanocrystalline materials. Transmission electron microscopy and atomistic simulations demonstrate that shear banding instability no longer afflicts the 5- to 10-nm-thick nanolaminate glassy layers during tensile deformation, which also act as high-capacity sinks for dislocations, enabling absorption of free volume and free energy transported by the dislocations; the amorphous-crystal interfaces exhibit unique inelastic shear (slip) transfer characteristics, fundamentally different from those of grain boundaries. Nanoscale metallic glass layers therefore may offer great benefits in engineering the plasticity of crystalline materials and opening new avenues for improving their strength and ductility.

| S-EPMC1899185 | biostudies-literature

Demonstration of thin film pair distribution function analysis (tfPDF) for the study of local structure in amorphous and crystalline thin films.

Project description:By means of normal-incidence, high-flux and high-energy X-rays, total scattering data for pair distribution function (PDF) analysis have been obtained from thin films (tf), suitable for local structure analysis. By using amorphous substrates as support for the films, the standard Rapid Acquisition PDF setup can be applied and the scattering signal from the film can be isolated from the total scattering data through subtraction of an independently measured background signal. No angular corrections to the data are needed, as would be the case for grazing incidence measurements. The 'tfPDF' method is illustrated through studies of as-deposited (i.e. amorphous) and crystalline FeSb3 films, where the local structure analysis gives insight into the stabilization of the metastable skutterudite FeSb3 phase. The films were prepared by depositing ultra-thin alternating layers of Fe and Sb, which interdiffuse and after annealing crystallize to form the FeSb3 structure. The tfPDF data show that the amorphous precursor phase consists of corner-sharing FeSb6 octahedra with motifs highly resembling the local structure in crystalline FeSb3. Analysis of the amorphous structure allows the prediction of whether the final crystalline product will form the FeSb3 phase with or without excess Sb present. The study thus illustrates how analysis of the local structure in amorphous precursor films can help to understand crystallization processes of metastable phases and opens for a range of new local structure studies of thin films.

| S-EPMC4547816 | biostudies-literature

Monitoring the Structure Evolution of Titanium Oxide Photocatalysts: From the Molecular Form via the Amorphous State to the Crystalline Phase.

Project description:Amorphous Tix Oy with high surface area has attracted significant interest as photocatalyst with higher activity in ultraviolet (UV) light-induced water splitting applications compared to commercial nanocrystalline TiO2 . Under photocatalytic operation conditions, the structure of the molecular titanium alkoxide precursor rearranges upon hydrolysis and leads to higher connectivity of the structure-building units. Structurally ordered domains with sizes smaller than 7 Å form larger aggregates. The experimental scattering data can be explained best with a structure model consisting of an anatase-like core and a distorted shell. Upon exposure to UV light, the white Tix Oy suspension turns dark corresponding to the reduction of Ti4+ to Ti3+ as confirmed by electron energy loss spectroscopy (EELS). Heat-induced crystallisation was followed by in situ temperature-dependent total scattering experiments. First, ordering in the Ti-O environment takes place upon to 350 °C. Above this temperature, the distorted anatase core starts to grow but the structure obtained at 400 °C is still not fully ordered.

| S-EPMC8456846 | biostudies-literature

Amorphous Blue Phase III: Structure, Materials, and Properties.

Project description:Blue phases (BPs) have a frustrated structure stabilized by chirality-dependent defects. They are classified into three categories: blue phase I (BPI), blue phase II (BPII), and blue phase III (BPIII). Among them, BPIII has recently attracted much attention due to its elusive amorphous structure and high-contrast electro-optical response. However, its structure has remained unelucidated, and the molecular design for stabilizing BPIII is still unclear. We present the following findings in this review. (1) BPIII is a spaghetti-like tangled arrangement of double-twist cylinders with characteristic dynamics. (2) Molecular biaxiality and flexibility contribute to stabilize BPIII. (3) BPIII exhibits submillisecond response, high contrast, and wide-viewing angle at room temperature without surface treatment or an optical compensation film. It was free from both hysteresis and residual transmittance. The electro-optical effects are explained in relation to the revealed structure of BPIII. Finally, we discuss the memory effect of a polymer network derived from the defects of BPIII.

| S-EPMC10972530 | biostudies-literature

Atomic-scale study of the amorphous-to-crystalline phase transition mechanism in GeTe thin films.

Project description:The underlying mechanism driving the structural amorphous-to-crystalline transition in Group VI chalcogenides is still a matter of debate even in the simplest GeTe system. We exploit the extreme sensitivity of 57Fe emission Mössbauer spectroscopy, following dilute implantation of 57Mn (T½ = 1.5 min) at ISOLDE/CERN, to study the electronic charge distribution in the immediate vicinity of the 57Fe probe substituting Ge (FeGe), and to interrogate the local environment of FeGe over the amorphous-crystalline phase transition in GeTe thin films. Our results show that the local structure of as-sputtered amorphous GeTe is a combination of tetrahedral and defect-octahedral sites. The main effect of the crystallization is the conversion from tetrahedral to defect-free octahedral sites. We discover that only the tetrahedral fraction in amorphous GeTe participates to the change of the FeGe-Te chemical bonds, with a net electronic charge density transfer of ~ 1.6 e/a0 between FeGe and neighboring Te atoms. This charge transfer accounts for a lowering of the covalent character during crystallization. The results are corroborated by theoretical calculations within the framework of density functional theory. The observed atomic-scale chemical-structural changes are directly connected to the macroscopic phase transition and resistivity switch of GeTe thin films.

| S-EPMC5558007 | biostudies-literature

Dense colloidal fluids form denser amorphous sediments.

Project description:We relate, by simple analytical centrifugation experiments, the density of colloidal fluids with the nature of their randomly packed solid sediments. We demonstrate that the most dilute fluids of colloidal hard spheres form loosely packed sediments, where the volume fraction of the particles approaches in frictional systems the random loose packing limit, ?RLP = 0.55. The dense fluids of the same spheres form denser sediments, approaching the so-called random close packing limit, ?RCP = 0.64. Our experiments, where particle sedimentation in a centrifuge is sufficiently rapid to avoid crystallization, demonstrate that the density of the sediments varies monotonically with the volume fraction of the initial suspension. We reproduce our experimental data by simple computer simulations, where structural reorganizations are prohibited, such that the rate of sedimentation is irrelevant. This suggests that in colloidal systems, where viscous forces dominate, the structure of randomly close-packed and randomly loose-packed sediments is determined by the well-known structure of the initial fluids of simple hard spheres, provided that the crystallization is fully suppressed.

| S-EPMC3625288 | biostudies-literature

From amorphous to crystalline: a universal strategy for structure regulation of high-entropy transition metal oxides.

Project description:High-entropy materials (HEMs) exhibit extensive application potential owing to their unique structural characteristics. Structure regulation is an effective strategy for enhancing material performance. However, the fabrication of HEMs by integrating five metal elements into a single crystalline phase remains a grand challenge, not to mention their structure regulation. Herein, an amorphous-to-crystalline transformation route is proposed to simultaneously achieve the synthesis and structure regulation of high-entropy metal oxides (HEMOs). Through a facile hydrothermal technique, five metal sources are uniformly integrated into amorphous carbon spheres, which are transformed to crystalline HEMOs after calcination. Importantly, by controlling ion diffusion and oxidation rates, HEMOs with different structures can be controllably achieved. As an example, HEMO of the five first-row transition metals CrMnFeCoNiO is synthesized through the amorphous-to-crystalline transformation route, and structure regulation from solid spheres to core-shell spheres, and then to hollow spheres, is successfully realized. Among the structures, the core-shell CrMnFeCoNiO exhibits enhanced lithium storage performance due to the component and structural advantages. Our work expands the synthesis methods for HEMs and provides a rational route for structure regulation, which brings them great potential as high-performance materials in energy storage and conversion.

| S-EPMC9930932 | biostudies-literature

Structure of the amorphous titania precursor phase of N-doped photocatalysts.

Project description:Amorphous titania samples prepared by ammonia solution neutralization of titanyl sulphate have been characterized by chemical and thermal analyses, and with reciprocal-space and real-space fitting of wide-angle synchrotron X-ray scattering data. A model that fits both the chemical and structural data comprises small segments of lepidocrocite-type layer that are offset by corner-sharing as in the monoclinic titanic acids H2Ti n O2n+1·mH2O. The amorphous phase composition that best fits the combined chemical and scattering data is [(NH4)3H21Ti20O52]·14H2O, where the formula within the brackets is the cluster composition and the H2O outside the brackets is physically adsorbed. The NH4 + cations are an integral part of the clusters and are bonded to layer anions at the corners of the offset layers, as occurs in the alkali metal stepped-layer titanates. The stepped-layer model is shown to give a consistent mechanism for the reaction of aqueous ammonia with solid hydrated titanyl sulphate, in which the amorphous product retains the exact size and shape of the reacting titanyl sulphate crystals.

| S-EPMC8695186 | 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