Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Theoretical Study on Trehalose + Water Mixtures for Dry Preservation Purposes.

ABSTRACT: The properties of trehalose + water mixtures are studied as a function of mixture composition and temperature using molecular dynamics simulations. As trehalose disaccharide has been proposed for dry preservation purposes, the objective of this work is to analyse the nanoscopic properties of the considered mixtures, in terms of aggregation, clustering, interactions energies, and local dynamics, and their relationships with hydrogen bonding. The reported results allow a detailed characterization of hydrogen bonding and its evolution with mixture composition and thus inferring the effects of trehalose on water structuring providing results to justify the mechanisms of trehalose acting as preservation agent.

SUBMITTER: Kumar A

PROVIDER: S-EPMC7145318 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A Theoretical Study on Trehalose + Water Mixtures for Dry Preservation Purposes.

Kumar Amit A Cincotti Alberto A Aparicio Santiago S

Molecules (Basel, Switzerland) 20200321 6

The properties of trehalose + water mixtures are studied as a function of mixture composition and temperature using molecular dynamics simulations. As trehalose disaccharide has been proposed for dry preservation purposes, the objective of this work is to analyse the nanoscopic properties of the considered mixtures, in terms of aggregation, clustering, interactions energies, and local dynamics, and their relationships with hydrogen bonding. The reported results allow a detailed characterization ...[more]

PMID: 32245231

Similar Datasets

Combined Experimental and Theoretical Study of Weak Polyelectrolyte Brushes in Salt Mixtures.

Project description:The swelling behavior of a hydrophobic poly(2diisopropylamino)ethyl methacrylate (PDPA) brush immersed in aqueous solutions of single and mixed salts has been investigated using ellipsometry and numerical self-consistent field (nSCF) theory. As a function of solution ionic strength, the osmotic and salted brush regimes of weak polyelectrolyte brushes as well as substantial specific anion effects in the presence of K+ salts of Cl-, NO3-, and SCN- are found. For solutions containing mixtures of NO3- and Cl-, the brush swelling is the same as one would expect on the basis of the concentration-weighted average of the brush behavior in the single salt solutions. However, in mixtures of SCN- and Cl-, the swelling response is more complicated and substantial divergence from ideal behavior is observed. Mean-field theory shows excellent qualitative agreement with the ellipsometry findings. nSCF reveals that for the SCN-/Cl- cases the swelling behavior of the PDPA brush most likely arises from the predominant localization of the weakly hydrated SCN- within the brush compared to the more strongly hydrated Cl-.

| S-EPMC6407915 | biostudies-literature

Properties of Aqueous Trehalose Mixtures: Glass Transition and Hydrogen Bonding.

Project description:Trehalose is a naturally occurring disaccharide known to remarkably stabilize biomacromolecules in the biologically active state. The stabilizing effect is typically observed over a large concentration range and affects many macromolecules including proteins, lipids, and DNA. Of special interest is the transition from aqueous solution to the dense and highly concentrated glassy state of trehalose that has been implicated in bioadaptation of different organisms toward desiccation stress. Although several mechanisms have been suggested to link the structure of the low water content glass with its action as an exceptional stabilizer, studies are ongoing to resolve which are most pertinent. Specifically, the role that hydrogen bonding plays in the formation of the glass is not well resolved. Here we model aqueous trehalose mixtures over a wide concentration range, using molecular dynamics simulations with two available force fields. Both force fields indicate glass transition temperatures and osmotic pressures that are close to experimental values, particularly at high trehalose contents. We develop and employ a methodology that allows us to analyze the thermodynamics of hydrogen bonds in simulations at different water contents and temperatures. Remarkably, this analysis is able to link the liquid to glass transition with changes in hydrogen bond characteristics. Most notably, the onset of the glassy state can be quantitatively related to the transition from weakly to strongly correlated hydrogen bonds. Our findings should help resolve the properties of the glass and the mechanisms of its formation in the presence of added macromolecules.

| S-EPMC7467637 | biostudies-literature

Silicate-mediated interstellar water formation: A theoretical study.

Project description:Water is one of the most abundant molecules in the form of solid ice phase in the different regions of the interstellar medium (ISM). This large abundance cannot be properly explained by using only traditional low temperature gas-phase reactions. Thus, surface chemical reactions are believed to be major synthetic channels for the formation of interstellar water ice. Among the different proposals, hydrogenation of atomic O (i.e., 2H + O → H2O) is a chemically "simple" and plausible reaction toward water formation occurring on the surfaces of interstellar grains. Here, novel theoretical results concerning the formation of water adopting this mechanism on the crystalline (010) Mg2SiO4 surface (a unequivocally identified interstellar silicate) are presented. The investigated reaction aims to simulate the formation of the first water ice layer covering the silicate core of dust grains. Adsorption of the atomic O as a first step of the reaction has been computed, results indicating that a peroxo ( O22- ) group is formed. The following steps involve the adsorption, diffusion and reaction of two successive H atoms with the adsorbed O atom. Results indicate that H diffusion on the surface has barriers of 4-6 kcal mol-1, while actual formation of OH and H2O present energy barriers of 22-23 kcal mol-1. Kinetic study results show that tunneling is crucial for the occurrence of the reactions and that formation of OH and H2O are the bottlenecks of the overall process. Several astrophysical implications derived from the theoretical results are provided as concluding remarks.

| S-EPMC6544534 | biostudies-literature

A Raman microspectroscopy study of water and trehalose in spin-dried cells.

Project description:Long-term storage of desiccated nucleated mammalian cells at ambient temperature may be accomplished in a stable glassy state, which can be achieved by removal of water from the biological sample in the presence of glass-forming agents including trehalose. The stability of the glass may be compromised due to a nonuniform distribution of residual water and trehalose within and around the desiccated cells. Thus, quantification of water and trehalose contents at the single-cell level is critical for predicting the glass formation and stability for dry storage. Using Raman microspectroscopy, we estimated the trehalose and residual water contents in the microenvironment of spin-dried cells. Individual cells with or without intracellular trehalose were embedded in a solid thin layer of extracellular trehalose after spin-drying. We found strong evidence suggesting that the residual water was bound at a 2:1 water/trehalose molar ratio in both the extracellular and intracellular milieus. Other than the water associated with trehalose, we did not find any more residual water in the spin-dried sample, intra- or extracellularly. The extracellular trehalose film exhibited characteristics of an amorphous state with a glass transition temperature of ?22°C. The intracellular milieu also dried to levels suitable for glass formation at room temperature. These findings demonstrate a method for quantification of water and trehalose in desiccated specimens using confocal Raman microspectroscopy. This approach has broad use in desiccation studies to carefully investigate the relationship of water and trehalose content and distribution with the tolerance to drying in mammalian cells.

| S-EPMC4241435 | biostudies-literature

How worms survive desiccation: Trehalose pro water.

Project description:While life requires water, many organisms, known as anhydrobiotes, can survive in the absence of water for extended periods of time. Although discovered 300 years ago, we know very little about the fascinating phenomenon of anhydrobiosis. In this paper, we summarize our previous findings on the desiccation tolerance of the Caenorhabditis elegans dauer larva. A special emphasis is given to the role of trehalose in protecting membranes against desiccation. We also propose a simple mechanism for this process.

| S-EPMC3670174 | biostudies-literature

Towards water-free biobanks: long-term dry-preservation at room temperature of desiccation-sensitive enzyme luciferase in air-dried insect cells.

Project description:Desiccation-tolerant cultured cells Pv11 derived from the anhydrobiotic midge embryo endure complete desiccation in an ametabolic state and resume their metabolism after rehydration. These features led us to develop a novel dry preservation technology for enzymes as it was still unclear whether Pv11 cells could preserve an exogenous enzyme in the dry state. This study shows that Pv11 cells protect an exogenous desiccation-sensitive enzyme, luciferase (Luc), preserving the enzymatic activity even after dry storage for 372 days at room temperature. A process including preincubation with trehalose, dehydration, storage, and rehydration allowed Pv11 (Pv11-Luc) cells stably expressing luciferase to survive desiccation and still emit luminescence caused by luciferase after rehydration. Luminescence produced by luciferase in Pv11-Luc cells after rehydration did not significantly decrease in presence of a translation inhibitor, showing that the activity did not derive from de novo enzyme synthesis following the resumption of cell metabolism. These findings indicate that the surviving Pv11 cells almost completely protect luciferase during desiccation. Lacking of the preincubation step resulted in the loss of luciferase activity after rehydration. We showed that preincubation with trehalose associated to induction of desiccation tolerance-related genes in Pv11 cells allowed effective in vivo preservation of enzymes in the dry state.

| S-EPMC5529557 | biostudies-literature

A microfluidic device for dry sample preservation in remote settings.

Project description:This paper describes a microfluidic device for dry preservation of biological specimens at room temperature that incorporates chemical stabilization matrices. Long-term stabilization of samples is crucial for remote medical analysis, biosurveillance, and archiving, but the current paradigm for transporting remotely obtained samples relies on the costly "cold chain" to preserve analytes within biospecimens. We propose an alternative approach that involves the use of microfluidics to preserve samples in the dry state with stabilization matrices, developed by others, that are based on self-preservation chemistries found in nature. We describe a SlipChip-based device that allows minimally trained users to preserve samples with the three simple steps of placing a sample at an inlet, closing a lid, and slipping one layer of the device. The device fills automatically, and a pre-loaded desiccant dries the samples. Later, specimens can be rehydrated and recovered for analysis in a laboratory. This device is portable, compact, and self-contained, so it can be transported and operated by untrained users even in limited-resource settings. Features such as dead-end and sequential filling, combined with a "pumping lid" mechanism, enable precise quantification of the original sample's volume while avoiding overfilling. In addition, we demonstrated that the device can be integrated with a plasma filtration module, and we validated device operations and capabilities by testing the stability of purified RNA solutions. These features and the modularity of this platform (which facilitates integration and simplifies operation) would be applicable to other microfluidic devices beyond this application. We envision that as the field of stabilization matrices develops, microfluidic devices will be useful for cost-effectively facilitating remote analysis and biosurveillance while also opening new opportunities for diagnostics, drug development, and other medical fields.

| S-EPMC3851311 | biostudies-literature

Sustaining dry surfaces under water.

Project description:Rough surfaces immersed under water remain practically dry if the liquid-solid contact is on roughness peaks, while the roughness valleys are filled with gas. Mechanisms that prevent water from invading the valleys are well studied. However, to remain practically dry under water, additional mechanisms need consideration. This is because trapped gas (e.g. air) in the roughness valleys can dissolve into the water pool, leading to invasion. Additionally, water vapor can also occupy the roughness valleys of immersed surfaces. If water vapor condenses, that too leads to invasion. These effects have not been investigated, and are critically important to maintain surfaces dry under water. In this work, we identify the critical roughness scale, below which it is possible to sustain the vapor phase of water and/or trapped gases in roughness valleys - thus keeping the immersed surface dry. Theoretical predictions are consistent with molecular dynamics simulations and experiments.

| S-EPMC4539549 | biostudies-literature

Theoretical Study of O2 Reduction and Water Oxidation in Multicopper Oxidases.

Project description:Recent electrochemical experiments have shown that the reduction of O2 can be driven backward to water oxidation, which is the first case that has been successfully demonstrated for an enzyme. To understand this ability of the enzyme, both the forward reduction and backward oxidation have been studied here. For the forward reaction, a mechanism similar to earlier studies was obtained. All steps of the full catalytic cycle were obtained for the first time, and it was shown that the explicit reduction steps contribute significantly to the rate-limiting step of the O-O bond cleavage. For the backward oxidation reaction, it was found that the mechanism of the O-O bond formation is not just the reverse of the reduction step where the O-O bond is cleaved for a protonated peroxide. The formation of two fully deprotonated oxo groups was found to be important, which leads to a large radical character for one of the oxo groups. For this possibility, it is important that the pKa of the water bound to the cofactor is quite high.

| S-EPMC7467714 | biostudies-literature

Hydrogen-bonding Interactions between Apigenin and Ethanol/Water: A Theoretical Study.

Project description:In this work, hydrogen-bonding interactions between apigenin and water/ethanol were investigated from a theoretical perspective using quantum chemical calculations. Two conformations of apigenin molecule were considered in this work. The following results were found. (1) For apigenin monomer, the molecular structure is non-planar, and all of the hydrogen and oxygen atoms can be hydrogen-bonding sites. (2) Eight and seven optimized geometries are obtained for apigenin (I)-H2O/CH3CH2OH and apigenin (II)-H2O/CH3CH2OH complexes, respectively. In apigenin, excluding the aromatic hydrogen atoms in the phenyl substituent, all other hydrogen atoms and the oxygen atoms form hydrogen-bonds with H2O and CH3CH2OH. (3) In apigenin-H2O/CH3CH2OH complexes, the electron density and the E(2) in the related localized anti-bonding orbital are increased upon hydrogen-bond formation. These are the cause of the elongation and red-shift of the X-H bond. The sum of the charge change transfers from the hydrogen-bond acceptor to donor. The stronger interaction makes the charge change more intense than in the less stable structures. (4) Most of the hydrogen-bonds in the complexes are electrostatic in nature. However, the C4-O5···H, C9-O4···H and C13-O2···H hydrogen-bonds have some degree of covalent character. Furthermore, the hydroxyl groups of the apigenin molecule are the preferred hydrogen-bonding sites.

| S-EPMC5048163 | 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