Browse
Submit Data
Databases
API
Help

Dataset Information

5 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Conformational Properties of Flaxseed Rhamnogalacturonan-I and Correlation between Primary Structure and Conformation.

ABSTRACT: The pectic polysaccharides extracted from flaxseed (Linum usitatissiumum L.) mucilage and kernel were characterized as rhamnogalacturonan-I (RG-I). In this study, the conformational characteristics of RG-I fractions from flaxseed mucilage and kernel were investigated, using a Brookhaven multi-angle light scattering instrument (batch mode) and a high-performance size exclusion chromatography (HPSEC) system coupled with Viscotek tetra-detectors (flow mode). The M_w of flaxseed mucilage RG-I (FM-R) was 285 kDa, and the structure-sensitive parameter (ρ) value of FM-R was calculated as 1.3, suggesting that the FM-R molecule had a star-like conformation. The M_w of flaxseed kernel RG-I (FK-R) was 550 kDa, and the structure-sensitive parameter (ρ) values ranged from 0.90 to 1.21, suggesting a sphere to star-like conformation with relatively higher segment density. The correlation between the primary structure and conformation of RG-I was further discussed to better understand the structure-function relationship, which helps the scale-up applications of pectins in food, pharmaceutical, or cosmetic industries.

SUBMITTER: Guo Q

PROVIDER: S-EPMC9269093 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Coypu insulin. Primary structure, conformation and biological properties of a hystricomorph rodent insulin.

Project description:Insulin from a hystricomorph rodent, coypu (Myocaster coypus), was isolated and purified to near homogeneity. Like the other insulins that have been characterized in this Suborder of Rodentia, coypu insulin also exhibits a very low (3%) biological potency, relative to pig insulin, on lipogenesis in isolated rat fat-cells. The receptor-binding affinity is significantly higher (5-8%) in rat fat-cells, in rat liver plasma membranes and in pig liver cells, indicating that the efficacy of coypu insulin on receptors is about 2-fold lower than that of pig insulin. The primary structures of the oxidized A- and B-chains were determined, and our sequence analysis confirms a previous report [Smith (1972) Diabetes 21, Suppl. 2, 457-460] that the C-terminus of the A-chain is extended by a single residue (i.e. aspartate-A22), in contrast with most other insulin sequences, which terminate at residue A21. In spite of a large number of amino acid substitutions (relative to mammalian insulins), computer-graphics model-building studies suggest a similar spatial arrangement for coypu insulin to that for pig insulin. The substitution of the zinc-co-ordinating site (B10-His----Gln) along with various substitutions on the intermolecular surfaces involved in the formation of higher aggregates are consistent with the observation that this insulin is predominantly 'monomeric' in nature. The c.d. spectrum of coypu insulin is relatively similar to those of casiragua insulin and of bovine insulin at low concentration.

| S-EPMC1147142 | biostudies-other

Correlation between the conformational states of F1-ATPase as determined from its crystal structure and single-molecule rotation.

Project description:F(1)-ATPase is a rotary molecular motor driven by ATP hydrolysis that rotates the gamma-subunit against the alpha(3)beta(3) ring. The crystal structures of F(1), which provide the structural basis for the catalysis mechanism, have shown essentially 1 stable conformational state. In contrast, single-molecule studies have revealed that F(1) has 2 stable conformational states: ATP-binding dwell state and catalytic dwell state. Although structural and single-molecule studies are crucial for the understanding of the molecular mechanism of F(1), it remains unclear as to which catalytic state the crystal structure represents. To address this issue, we introduced cysteine residues at betaE391 and gammaR84 of F(1) from thermophilic Bacillus PS3. In the crystal structures of the mitochondrial F(1), the corresponding residues in the ADP-bound beta (beta(DP)) and gamma were in direct contact. The betaE190D mutation was additionally introduced into the beta to slow ATP hydrolysis. By incorporating a single copy of the mutant beta-subunit, the chimera F(1), alpha(3)beta(2)beta(E190D/E391C)gamma(R84C), was prepared. In single-molecule rotation assay, chimera F(1) showed a catalytic dwell pause in every turn because of the slowed ATP hydrolysis of beta(E190D/E391C). When the mutant beta and gamma were cross-linked through a disulfide bond between betaE391C and gammaR84C, F(1) paused the rotation at the catalytic dwell angle of beta(E190D/E391C), indicating that the crystal structure represents the catalytic dwell state and that beta(DP) is the catalytically active form. The former point was again confirmed in experiments where F(1) rotation was inhibited by adenosine-5'-(beta,gamma-imino)-triphosphate and/or azide, the most commonly used inhibitors for the crystallization of F(1).

| S-EPMC2603257 | biostudies-literature

Liposome/DNA systems: correlation between hydrophobicity and DNA conformational changes.

Project description:In a previous work, we found that liposome hydrophobicity could affect deoxyribonucleic acid (DNA) association efficiency. Now, we have focused on the possible correlation between liposome hydrophobicity and DNA conformation. DNA lyophilized with cationic vesicles with high hydrophobicity changes its conformation into a more condensed form, probably the C form. With noncharged vesicles, it changes its conformation from B to a partial A form. These results contribute to a better understanding of the interaction between DNA and lipids, suggesting there is direct relationship between hydrophobicity and DNA conformation changes: The higher the hydrophobicity factor, the more pronounced the changes in DNA form, to a more condensed form.

| S-EPMC2577743 | biostudies-other

Correlation between particle size/domain structure and magnetic properties of highly crystalline Fe3O4 nanoparticles.

Project description:Highly crystalline single-domain magnetite Fe3O4 nanoparticles (NPs) are important, not only for fundamental understanding of magnetic behaviour, but also for their considerable potential applications in biomedicine and industry. Fe3O4 NPs with sizes of 10-300?nm were systematically investigated to reveal the fundamental relationship between the crystal domain structure and the magnetic properties. The examined Fe3O4 NPs were prepared under well-controlled crystal growth conditions using a large-scale liquid precipitation method. The crystallite size of cube-like NPs estimated from X-ray diffraction pattern increased linearly as the particle size (estimated by transmission electron microscopy) increased from 10 to 64.7?nm, which indicates that the NPs have a single-domain structure. This was further confirmed by the uniform lattice fringes. The critical size of approximately 76?nm was obtained by correlating particle size with both crystallite size and magnetic coercivity; this was reported for the first time in this study. The coercivity of cube-like Fe3O4 NPs increased to a maximum of 190?Oe at the critical size, which suggests strong exchange interactions during spin alignment. Compared with cube-like NPs, sphere-like NPs have lower magnetic coercivity and remanence values, which is caused by the different orientations of their polycrystalline structure.

| S-EPMC5577113 | biostudies-other

Correlation between supercoiling and conformational motions of the bacterial flagellar filament.

Project description:The bacterial flagellar filament is a very large macromolecular assembly of a single protein, flagellin. Various supercoiled states of the filament exist, which are formed by two structurally different conformations of flagellin in different ratios. We investigated the correlation between supercoiling of the protofilaments and molecular dynamics in the flagellar filament using quasielastic and elastic incoherent neutron scattering on the picosecond and nanosecond timescales. Thermal fluctuations in the straight L- and R-type filaments were measured and compared to the resting state of the wild-type filament. Amplitudes of motion on the picosecond timescale were found to be similar in the different conformational states. Mean-square displacements and protein resilience on the 0.1 ns timescale demonstrate that the L-type state is more flexible and less resilient than the R-type, whereas the wild-type state lies in between. Our results provide strong support that supercoiling of the protofilaments in the flagellar filament is determined by the strength of molecular forces in and between the flagellin subunits.

| S-EPMC3824299 | biostudies-literature

Correlation between the conformation space and the sequence space of Peptide chain.

Project description:Effects of point mutations are investigated in a computer model ofsequence selection. In the model, sequences are selected according totheir functional ability defined by the configuration at the active site.Through such functional selection on the local configuration, sequenceswhich fold globally into a unique conformation can be selected from randomsequences. The selected sequence accepts many point mutations as neutralmutations. More structurally fluctuating sites in the chain accept alarger variety of point mutations, which shows correlation between theconformational fluctuation and the sequence fluctuation.

| S-EPMC3456737 | biostudies-other

A correlation between secondary structure and rheological properties of low-density lipoproteins at air/water interfaces.

Project description:The secondary structure of apolipoprotein B-100 is studied within the bulk phase and at the air/water interface. In these "in viro" experiments, infrared reflection absorption spectroscopy (IRRAS) study was performed at the air/water interface while circular dichroism (CD) was conducted in the bulk phase. In the bulk phase, the conformational structure containing a significant amount of ?-structure, whereas varying amount of ?-helix, unordered structures, and ?-sheet were observed at the air/water interface depending on the low-density lipoprotein (LDL) film interfacial pressure. The present IRRAS results demonstrate the importance of interfacial pressure-induced structural conformations on the apoB-100. A correlation between the secondary structure of the apoB-100 protein and the monomolecular film elasticity at the air/water interface was also established. The orientation of apoB-100 with respect to the LDL film-normal was found to depend on the interfacial pressure exhibited by the monomolecular film. These results may shed light on LDL's pivotal role in the progression of atherosclerotic coronary artery disease as demonstrated previously by clinical trials.

| S-EPMC6104898 | biostudies-other

Ionogels Based on Poly(methyl methacrylate) and Metal-Containing Ionic Liquids: Correlation between Structure and Mechanical and Electrical Properties.

Project description:Ionogels (IGs) based on poly(methyl methacrylate) (PMMA) and the metal-containing ionic liquids (ILs) bis-1-butyl-3-methlimidazolium tetrachloridocuprate(II), tetrachloride cobaltate(II), and tetrachlorido manganate(II) have been synthesized and their mechanical and electrical properties have been correlated with their microstructure. Unlike many previous examples, the current IGs show a decreasing stability in stress-strain experiments on increasing IL fractions. The conductivities of the current IGs are lower than those observed in similar examples in the literature. Both effects are caused by a two-phase structure with micrometer-sized IL-rich domains homogeneously dispersed an IL-deficient continuous PMMA phase. This study demonstrates that the IL-polymer miscibility and the morphology of the IGs are key parameters to control the (macroscopic) properties of IGs.

| S-EPMC4813247 | biostudies-literature

Coupling between myosin head conformation and the thick filament backbone structure.

Project description:The recent high-resolution structure of the thick filament from Lethocerus asynchronous flight muscle shows aspects of thick filament structure never before revealed that may shed some light on how striated muscles function. The phenomenon of stretch activation underlies the function of asynchronous flight muscle. It is most highly developed in flight muscle, but is also observed in other striated muscles such as cardiac muscle. Although stretch activation is likely to be complex, involving more than a single structural aspect of striated muscle, the thick filament itself, would be a prime site for regulatory function because it must bear all of the tension produced by both its associated myosin motors and any externally applied force. Here we show the first structural evidence that the arrangement of myosin heads within the interacting heads motif is coupled to the structure of the thick filament backbone. We find that a change in helical angle of 0.16° disorders the blocked head preferentially within the Lethocerus interacting heads motif. This observation suggests a mechanism for how tension affects the dynamics of the myosin heads leading to a detailed hypothesis for stretch activation and shortening deactivation, in which the blocked head preferentially binds the thin filament followed by the free head when force production occurs.

| S-EPMC5733691 | biostudies-literature

Correlation between spin structure oscillations and domain wall velocities.

Project description:Magnetic sensing and logic devices based on the motion of magnetic domain walls rely on the precise and deterministic control of the position and the velocity of individual magnetic domain walls in curved nanowires. Varying domain wall velocities have been predicted to result from intrinsic effects such as oscillating domain wall spin structure transformations and extrinsic pinning due to imperfections. Here we use direct dynamic imaging of the nanoscale spin structure that allows us for the first time to directly check these predictions. We find a new regime of oscillating domain wall motion even below the Walker breakdown correlated with periodic spin structure changes. We show that the extrinsic pinning from imperfections in the nanowire only affects slow domain walls and we identify the magnetostatic energy, which scales with the domain wall velocity, as the energy reservoir for the domain wall to overcome the local pinning potential landscape.

| S-EPMC3759078 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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