Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Solvation of Glucose, Trehalose, and Sucrose by the Soft Sticky Dipole-Quadrupole-Octupole Water Model.

ABSTRACT: Water structure around sugars modeled by partial charges is compared for soft-sticky dipole-quadrupole-octupole (SSDQO), a fast single-site multipole model, and commonly used multi-site models in Monte Carlo simulations. Radial distribution functions and coordination numbers of all the models indicate similar hydration by hydrogen-bond donor and acceptor waters. However, the new optimized SSDQO1 parameters as well as TIP4P-Ew and TIP5P predict a "lone-pair" orientation for the water accepting the sugar hydroxyl hydrogen bond that is more consistent with the limited experimental data than the "dipole" orientation in SPC/E, which has important implications for studies of the cryoprotectant properties of sugars.

SUBMITTER: Te JA

PROVIDER: S-EPMC2975465 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Solvation of Glucose, Trehalose, and Sucrose by the Soft Sticky Dipole-Quadrupole-Octupole Water Model.

Te Jerez A JA Tan Ming-Liang ML Ichiye Toshiko T

Chemical physics letters 20100501 4-6

Water structure around sugars modeled by partial charges is compared for soft-sticky dipole-quadrupole-octupole (SSDQO), a fast single-site multipole model, and commonly used multi-site models in Monte Carlo simulations. Radial distribution functions and coordination numbers of all the models indicate similar hydration by hydrogen-bond donor and acceptor waters. However, the new optimized SSDQO1 parameters as well as TIP4P-Ew and TIP5P predict a "lone-pair" orientation for the water accepting th ...[more]

PMID: 21072255

Similar Datasets

UNDERSTANDING STRUCTURAL EFFECTS OF MULTIPOLE MOMENTS ON AQUEOUS SOLVATION OF IONS USING THE SOFT-STICKY DIPOLE-QUADRUPOLE-OCTUPOLE WATER MODEL.

Project description:The effects of water multipole moments on the aqueous solvation of ions were determined in Monte Carlo simulations using soft-sticky dipole-quadrupole-octupole (SSDQO) water. Water molecules formed linear hydrogen bonds to Cl(-) using the new SSDQO1 parameters, similar to multi-site models. However, the dipole vector was tilted rather than parallel to the oxygen-Na(+) internuclear vector as in most multi-site model, while experiment and ab initio molecular dynamics simulations generally indicate a range of values between tilted and parallel. By varying the multipoles in SSDQO, the octupole was found to determine the orientation around Na(+). Moreover, analysis of the multipoles of more conventional models is predictive of their performance as solvents.

| S-EPMC2975461 | biostudies-literature

Temperature and pressure dependence of the optimized soft-sticky dipole-quadrupole-octupole water model.

Project description:The soft-sticky dipole-quadrupole-octupole (SSDQO) potential energy function for a coarse-grained single-site water model has Lennard-Jones interactions and an approximate multipole expansion for the electrostatics. Here, the Lennard-Jones parameters and multipole moments of SSDQO were optimized so that the structural, thermodynamic, dynamic, and dielectric properties agreed with experimental values of liquid water at ambient conditions. Using these parameters, the temperature and pressure dependence of various properties were shown to be in good agreement with experiment, including a temperature of maximum density at approximately 260 K. This new parametrization, referred to as SSDQO1, is both computationally faster and generally more accurate over a wide range of conditions than traditional three-site water models, which demonstrates that a model with a single dipole, quadrupole, and octupole on each water molecule can reproduce the tetrahedral hydrogen bonded network of water.

| S-EPMC2855697 | biostudies-other

Rates of spontaneous cleavage of glucose, fructose, sucrose, and trehalose in water, and the catalytic proficiencies of invertase and trehalas.

Project description:Most of the early experimental work on enzyme kinetics was based on the properties of yeast invertase (beta-fructo-furanosidase, EC 3.2.1.26), whose robust activity(1) (together with the availability of a continuous polarimetric assay) enabled Michaelis and Menten to establish the existence of a quantitative relationship between the rate of an enzyme reaction and the concentration of its substrate.(2) To appreciate the proficiency of an enzyme as a catalyst, it is also desirable to have information about the relative rates of the catalyzed and uncatalyzed reactions.(3) Surprisingly, the literature discloses no report of the rate of spontaneous hydrolysis of sucrose (although there have been many studies of the acid-catalyzed reaction).(4) That information would be of special interest in view of the remarkable resistance to hydrolysis (t1/2 approximately 10(7) y),(5) of the 1-4 "head-to-tail" glycosidic linkages that join the common glucose polymers cellulose, chitin, amylose, and glycogen. Thus, polysaccharide hydrolases (e.g., beta-amylase) generate the largest rate enhancements that are known to be produced by hydrolytic enzymes that operate without the assistance of metals or other cofactors.(6) Here, we describe the uncatalyzed hydrolysis of sucrose and trehalose, in which the constituent monosaccharides are symmetrically joined, by a "head-to-head" glycosidic linkage between their carbonyl groups (Chart ).

| S-EPMC2664835 | biostudies-other

Excited-State Dipole and Quadrupole Moments: TD-DFT versus CC2.

Project description:The accuracies of the excited-state dipole and quadrupole moments obtained by TD-DFT are assessed by considering 16 different exchange-correlation functionals and more than 30 medium and large molecules. Except for excited-state presenting a significant charge-transfer character, a relatively limited dependency on the nature of the functional is found. It also turns out that while DFT ground-state dipole moments tend to be too large, the reverse trend is obtained for their excited-state counterparts, at least when hybrid functionals are used. Consequently, the TD-DFT excess dipole moments are often too small, an error that can be fortuitously corrected for charge-transfer transition by selecting a pure or a hybrid functional containing a small share of exact exchange. This error-cancelation phenomena explains the contradictory conclusions obtained in previous investigations. Overall, the largest correlation between CC2 and TD-DFT excess dipoles is obtained with M06-2X, but at the price of a nearly systematic underestimation of this property by ca. 1 D. For the excess quadrupole moments, the average errors are of the order of 0.2-0.6 D·Å for the set of small aromatic systems treated.

| S-EPMC4980690 | biostudies-literature

Structural Comparison between Sucrose and Trehalose in Aqueous Solution.

Project description:The two sugar molecules sucrose and trehalose are both considered as stabilizing molecules for the purpose of preserving biological materials during, for example, lyophilization or cryo-preservation. Although these molecules share a similar molecular structure, there are several important differences in their properties when they interact with water, such as differences in solubility, viscosity, and glass transition temperature. In general, trehalose has been shown to be more efficient than other sugar molecules in preserving different biological molecules against stress, and thus by investigating how these two disaccharides differ in their water interaction, it is possible to further understand what makes trehalose special in its stabilizing properties. For this purpose, the structure of aqueous solutions of these disaccharides was studied by using neutron and X-ray diffraction in combination with empirical potential structure refinement (EPSR) modeling. The results show that there are surprisingly few differences in the overall structure of the solutions, although there are indications for that trehalose perturbs the water structure slightly more than sucrose.

| S-EPMC7311057 | biostudies-literature

The sucrose-trehalose 6-phosphate (Tre6P) nexus: specificity and mechanisms of sucrose signalling by Tre6P.

Project description:Trehalose 6-phosphate (Tre6P), the intermediate of trehalose biosynthesis, has a profound influence on plant metabolism, growth, and development. It has been proposed that Tre6P acts as a signal of sugar availability and is possibly specific for sucrose status. Short-term sugar-feeding experiments were carried out with carbon-starved Arabidopsis thaliana seedlings grown in axenic shaking liquid cultures. Tre6P increased when seedlings were exogenously supplied with sucrose, or with hexoses that can be metabolized to sucrose, such as glucose and fructose. Conditional correlation analysis and inhibitor experiments indicated that the hexose-induced increase in Tre6P was an indirect response dependent on conversion of the hexose sugars to sucrose. Tre6P content was affected by changes in nitrogen status, but this response was also attributable to parallel changes in sucrose. The sucrose-induced rise in Tre6P was unaffected by cordycepin but almost completely blocked by cycloheximide, indicating that de novo protein synthesis is necessary for the response. There was a strong correlation between Tre6P and sucrose even in lines that constitutively express heterologous trehalose-phosphate synthase or trehalose-phosphate phosphatase, although the Tre6P:sucrose ratio was shifted higher or lower, respectively. It is proposed that the Tre6P:sucrose ratio is a critical parameter for the plant and forms part of a homeostatic mechanism to maintain sucrose levels within a range that is appropriate for the cell type and developmental stage of the plant.

| S-EPMC3935566 | biostudies-literature

The large quadrupole of water molecules.

Project description:Many quantum mechanical calculations indicate water molecules in the gas and liquid phase have much larger quadrupole moments than any of the common site models of water for computer simulations. Here, comparisons of multipoles from quantum mechanical∕molecular mechanical (QM∕MM) calculations at the MP2∕aug-cc-pVQZ level on a B3LYP∕aug-cc-pVQZ level geometry of a waterlike cluster and from various site models show that the increased square planar quadrupole can be attributed to the p-orbital character perpendicular to the molecular plane of the highest occupied molecular orbital as well as a slight shift of negative charge toward the hydrogens. The common site models do not account for the p-orbital type electron density and fitting partial charges of TIP4P- or TIP5P-type models to the QM∕MM dipole and quadrupole give unreasonable higher moments. Furthermore, six partial charge sites are necessary to account reasonably for the large quadrupole, and polarizable site models will not remedy the problem unless they account for the p-orbital in the gas phase since the QM calculations show it is present there too. On the other hand, multipole models by definition can use the correct multipoles and the electrostatic potential from the QM∕MM multipoles is much closer than that from the site models to the potential from the QM∕MM electron density. Finally, Monte Carlo simulations show that increasing the quadrupole in the soft-sticky dipole-quadrupole-octupole multipole model gives radial distribution functions that are in good agreement with experiment.

| S-EPMC3081860 | biostudies-other

The inhibition of fibril formation of lysozyme by sucrose and trehalose.

Project description:The two disaccharides, trehalose and sucrose, have been compared in many studies due to their structural similarity. Both possess the ability to stabilise and reduce aggregation of proteins. Trehalose has also been shown to inhibit the formation of highly structured protein aggregates called amyloid fibrils. This study aims to compare how the thermal stability of the protein lysozyme at low pH (2.0 and 3.5) is affected by the presence of the two disaccharides. We also address the anti-aggregating properties of the disaccharides and their inhibitory effects on fibril formation. Differential scanning calorimetry confirms that the thermal stability of lysozyme is increased by the presence of trehalose or sucrose. The effect is slightly larger for sucrose. The inhibiting effects on protein aggregation are investigated using small-angle X-ray scattering which shows that the two-component system consisting of lysozyme and water (Lys/H2O) at pH 2.0 contains larger aggregates than the corresponding system at pH 3.5 as well as the sugar containing systems. In addition, the results show that the particle-to-particle distance in the sugar containing systems (Lys/Tre/H2O and Lys/Suc/H2O) at pH 2.0 is longer than at pH 3.5, suggesting larger protein aggregates in the former. Finally, the characteristic distance separating β-strands in amyloid fibrils is observed for the Lys/H2O system at pH 2.0, using wide-angle X-ray scattering, while it is not clearly observed for the sugar containing systems. This study further shows that the two disaccharides stabilise the native fold of lysozyme by increasing the denaturation temperature. However, other factors, such as a weakening of hydrophobic interactions and hydrogen bonding between proteins, might also play a role in their inhibitory effect on amyloid fibril formation.

| S-EPMC11017192 | biostudies-literature

Light Guidance Aided by the Toroidal Dipole and the Magnetic Quadrupole in Silicon Slotted-Disk Chains.

Project description:Far-field scattering of high-index nanoparticles can be hugely reduced via interference of multipolar moments giving rise to the so-called anapole states. It has been suggested that this reduced scattering can contribute to efficient transmission along periodic chains of such nanoparticles. In this work, we analyze via numerical simulation and experiments the transmission of light along chains of regular and slotted silicon disks in the frequency region over the light cone. We do not observe transmission at wavelengths corresponding to the excitation of the first electric anapole for regular disks. However, large transmission along straight and curved chains is observed for slotted disks due to the simultaneous excitation of the toroidal dipole and magnetic quadrupole modes in the disks. Photonic band calculations unveil that such large transmission can be ascribed to leaky resonances, though bound states in the continuum do not appear in the structures under analysis. Experiments at telecom wavelengths using silicon disk chains confirm the numerical results for straight and bent chains. Our results provide new insights into the role of radiationless states in light guidance along nanoparticle chains and offer new avenues to utilize Mie resonances of simple nanophotonic structures for on-chip dielectric photonics.

| S-EPMC10021020 | biostudies-literature

Urea-Water Solvation Forces on Prion Structures.

Project description:Solvation forces are crucial determinants in the equilibrium between the folded and unfolded state of proteins. Particularly interesting are the solvent forces of denaturing solvent mixtures on folded and misfolded states of proteins involved in neurodegeneration. The C-terminal globular domain of the ovine prion protein (1UW3) and its analogue H2H3 in the α-rich and β-rich conformation were used as model structures to study the solvation forces in 4 M aqueous urea using molecular dynamics. The model structures display very different secondary structures and solvent exposures. Most protein atoms favor interactions with urea over interactions with water. The force difference between protein-urea and protein-water interactions correlates with hydrophobicity; i.e., urea interacts preferentially with hydrophobic atoms, in agreement with results from solvent transfer experiments. Solvent Shannon entropy maps illustrate the mobility gradient of the urea-water mixture from the first solvation shell to the bulk. Single urea molecules replace water in the first solvation shell preferably at locations of relatively high solvent entropy.

| S-EPMC3466777 | 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