Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions.

ABSTRACT: The biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte-TMAO (trimethylamine N-oxide) and destabilizing osmolyte-urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations. We isolated the spectroscopic share of water molecules that are simultaneously under the influence of peptide and osmolyte and determined the structural and energetic properties of these water molecules. Our experimental and computational results revealed that the changes in the structure of water around peptides, caused by the presence of stabilizing or destabilizing osmolyte, are significantly different for both NAGMA and diglycine. The main factor determining the influence of osmolytes on peptides is the structural-energetic similarity of their hydration spheres. We showed that the chosen peptides can serve as models for various fragments of the protein surface: NAGMA for the protein backbone and diglycine for the protein surface with polar side chains.

SUBMITTER: Panuszko A

PROVIDER: S-EPMC8431001 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Effect of Buffer on Protein Stability in Aqueous Solutions: A Simple Protein Aggregation Model.

Project description:Liquid-liquid phase separation (LLPS) of proteins has recently been associated with the onset of numerous diseases. Despite several studies in this area of protein aggregation, buffer-specific effects always seem to be overlooked. In this study we investigated the influence of buffers on the phase stability of hen egg-white lysozyme (HEWL) and its respective protein-protein interactions by measuring the cloud point temperature, second virial coefficient, and interaction diffusion coefficient of several HEWL-buffer solutions (MOPS, phosphate, HEPES, cacodylate) at pH 7.0. The results indicate that the buffer molecules, depending on their hydration, adsorb on the protein surface, and modulate their electrostatic stability. The obtained information was used to extend the recently developed coarse-grained protein model to incorporate buffer-specific effects. Treated by Wertheim's perturbation theory the model qualitatively correctly predicted the experimentally observed phase separation of all investigated HEWL-buffer solutions, and further allowed us to predict the phase stability of protein formulations even in experimentally unattainable conditions. Since the theory can be straightforwardly extended to include multiple components it presents a useful tool to study protein aggregation in crowded cell-like systems.

| S-EPMC8041305 | biostudies-literature

Simple method for quantification of anionic biosurfactants in aqueous solutions.

Project description:Biosurfactants are microbial products that have applications as cleaning agents, emulsifiers, and dispersants. Detection and quantification of biosurfactants can be done by various methods, including colorimetric tests, high performance liquid chromatography (HPLC) coupled to several types of detectors, and tests that take advantage of biosurfactants reducing surface tension of aqueous liquids, allowing for spreading and droplet formation of oils. We present a new and simple method for quantifying biosurfactants by their ability, on paper, to reduce surface tension of aqueous solutions, causing droplet dispersion on an oiled surface in correlation with biosurfactant content. We validated this method with rhamnolipids, surfactin, sophorolipids, and ananatoside B; all are anionic microbial surfactants. Linear ranges for quantification in aqueous solutions for all tested biosurfactants were between 10 and 500 µM. Our method showed time-dependent biosurfactant accumulation in cultures of Pseudomonas aeruginosa strains PA14 and PAO1, and Burkholderia thailandensis E264. Mutants in genes responsible for surfactant production showed negligible activity on oiled paper. In summary, our simple assay provides the opportunity to quantify biosurfactant contents of aqueous solutions, for a diversity of surfactants, by means readily available in any laboratory.

| S-EPMC10598384 | biostudies-literature

A simple one-step procedure to synthesise gold nanostars in concentrated aqueous surfactant solutions.

Project description:Due to the enhanced electromagnetic field at the tips of metal nanoparticles, the spiked structure of gold nanostars (AuNSs) is promising for surface-enhanced Raman scattering (SERS). Therefore, the challenge is the synthesis of well designed particles with sharp tips. The influence of different surfactants, i.e., dioctyl sodium sulfosuccinate (AOT), sodium dodecyl sulfate (SDS), and benzylhexadecyldimethylammonium chloride (BDAC), as well as the combination of surfactant mixtures on the formation of nanostars in the presence of Ag+ ions and ascorbic acid was investigated. By varying the amount of BDAC in mixed micelles the core/spike-shell morphology of the resulting AuNSs can be tuned from small cores to large ones with sharp and large spikes. The concomitant red-shift in the absorption toward the NIR region without losing the SERS enhancement enables their use for biological applications and for time-resolved spectroscopic studies of chemical reactions, which require a permanent supply with a fresh and homogeneous solution. HRTEM micrographs and energy-dispersive X-ray (EDX) experiments allow us to verify the mechanism of nanostar formation according to the silver underpotential deposition on the spike surface in combination with micelle adsorption.

| S-EPMC9069482 | biostudies-literature

Improved post thaw function and genetic changes for mesenchymal stromal cells cryopreserved using multicomponent osmolyte solutions

Project description:We report genome-wide expression changes that occur in H9-iMSCs frozen with different freezing methods that include DMSO and non-DMSO experimental solutions such as SGC (sucrose-glycerol-creatinine, SMC (sucrose-mannitol-creatinine), and SGI (sucrose-mannitol-isoleucine). mRNA-Seq analysis shows that DMSO samples cluster with fresh samples in the same clade, while all samples using the experimental solutions cluster together. In addition, we also see that cells frozen using experimental solutions have upregulation of a number of key molecular function pathways including extracellular matrix structural genes, receptor binding, and growth factor expression.

2016-12-30 | GSE88946 | GEO

PeptideBuilder: A simple Python library to generate model peptides.

Project description:We present a simple Python library to construct models of polypeptides from scratch. The intended use case is the generation of peptide models with pre-specified backbone angles. For example, using our library, one can generate a model of a set of amino acids in a specific conformation using just a few lines of python code. We do not provide any tools for energy minimization or rotamer packing, since powerful tools are available for these purposes. Instead, we provide a simple Python interface that enables one to add residues to a peptide chain in any desired conformation. Bond angles and bond lengths can be manipulated if so desired, and reasonable values are used by default.

| S-EPMC3661355 | biostudies-literature

Hydration of Oxometallate Ions in Aqueous Solution.

Project description:The strength of hydrogen bonding to and structure of hydrated oxometallate ions in aqueous solution have been studied by double difference infrared (DDIR) spectroscopy and large-angle X-ray scattering (LAXS), respectively. Anions are hydrated by accepting hydrogen bonds from the hydrating water molecules. The oxygen atom of the permanganate and perrhenate ions form weaker and longer hydrogen bonds to water than the hydrogen bonds in bulk water (i.e., they act as structure breakers), while the oxygen atoms of the chromate, dichromate, molybdate, tungstate, and hydrogenvanadate ions form hydrogen bonds stronger than those in bulk water (i.e., they act as structure makers). The oxometallate ions form one hydration shell distinguishable from bulk water as determined by DDIR spectroscopy and LAXS. The hydration of oxoanions results in X-O bond distances ca. 0.02 Å longer than those in unsolvated ions in the solid state not involved in strong bonding to counterions. The oxygens of oxoanions with a central atom from the second and third series in the periodic table and the hydrogenvanadate ion hydrogen bind three hydrating water molecules, while oxygens of oxoanions with a heavier central atom only form hydrogen bonds to two water molecules.

| S-EPMC7467666 | biostudies-literature

Simple Approach to Enhance Green Tea Epigallocatechin Gallate Stability in Aqueous Solutions and Bioavailability: Experimental and Theoretical Characterizations.

Project description:Because of its antioxidant, antimutagenic, and anti-infectious properties, epigallocatechin gallate (EGCG) is the most interesting compound among the green tea catechins polyphenols. However, its health effects are inconclusive due to its very low bioavailability, largely due to a particular instability that does not allow EGCG to reach the potency required for clinical developments. Over the last decade, many efforts have been made to improve the stability and bioavailability of EGCG using complex delivery systems such as nanotechnology, but these efforts have not been successful and easy to translate to industrial use. To meet the needs of a large-scale clinical trial requiring EGCG in a concentrated solution to anticipate swallowing impairments, we developed an EGCG-based aqueous solution in the simplest way while trying to circumvent EGCG instability. The solution was thoroughly characterized to sort out the unexpected stability outcome by combining experimental (HPLC-UV-mass spectrometry and infrared spectroscopy) and computational (density functional theory) studies. Against all odds, the EGCG-sucrose complex under certain conditions may have prevented EGCG from degradation in aqueous media. Indeed, in agreement with the ICH guidelines, the formulated solution was shown to be stable up to at least 24 months under 2-8 °C and at ambient temperature. Furthermore, considerable improvement in bioavailability in rats, against EGCG powder formulated in hard-gel capsules, was shown after gavage. Thus, the proposed formulation may provide an easily implementable platform to administer EGCG in the context of clinical development.

| S-EPMC8706847 | biostudies-literature

ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions.

Project description:A new implicit solvation model for use in Monte Carlo simulations of polypeptides is introduced. The model is termed ABSINTH for self-Assembly of Biomolecules Studied by an Implicit, Novel, and Tunable Hamiltonian. It is designed primarily for simulating conformational equilibria and oligomerization reactions of intrinsically disordered proteins in aqueous solutions. The paradigm for ABSINTH is conceptually similar to the EEF1 model of Lazaridis and Karplus (Proteins 1999, 35, 133). In ABSINTH, the transfer of a polypeptide solute from the gas phase into a continuum solvent is the sum of a direct mean field interaction (DMFI), and a term to model the screening of polar interactions. Polypeptide solutes are decomposed into a set of distinct solvation groups. The DMFI is a sum of contributions from each of the solvation groups, which are analogs of model compounds. Continuum-mediated screening of electrostatic interactions is achieved using a framework similar to the one used for the DMFI. Promising results are shown for a set of test cases. These include the calculation of NMR coupling constants for short peptides, the assessment of the thermal stability of two small proteins, reversible folding of both an alpha-helix and a beta-hairpin forming peptide, and the polymeric properties of intrinsically disordered polyglutamine peptides of varying lengths. The tests reveal that the computational expense for simulations with the ABSINTH implicit solvation model increase by a factor that is in the range of 2.5-5.0 with respect to gas-phase calculations.

| S-EPMC2670230 | biostudies-literature

Characterizing modes of action and interaction for multicomponent osmolyte solutions on Jurkat cells.

Project description:This study examined the post-thaw recovery of Jurkat cells cryopreserved in three combinations of five osmolytes including trehalose, sucrose, glycerol, mannitol, and creatine. Cellular response was characterized using low-temperature Raman spectroscopy, and variation of post-thaw recovery was analyzed using statistical modeling. Combinations of osmolytes displayed distinct trends of post-thaw recovery, and a nonlinear relationship between compositions and post-thaw recovery was observed, suggesting interactions not only between different solutes but also between solutes and cells. The post-thaw recovery for optimized cryoprotectants in different combinations of osmolytes at a cooling rate of 1°C/min was comparable to that measured with 10% dimethyl sulfoxide. Statistical modeling was used to understand the importance of individual osmolytes as well as interactions between osmolytes on post-thaw recovery. Both higher concentrations of glycerol and certain interactions between sugars and glycerol were found to typically increase the post-thaw recovery. Raman images showed the influence of osmolytes and combinations of osmolytes on ice crystal shape, which reflected the interactions between osmolytes and water. Differences in the composition also influenced the presence or absence of intracellular ice formation, which could also be detected by Raman. These studies help us understand the modes of action for cryoprotective agents in these osmolyte solutions.

| S-EPMC7720914 | biostudies-literature

Osmolyte transporter expression is reduced in photoaged human skin: Implications for skin hydration in aging.

Project description:Aging is characterized by the deterioration of tissue structure and function. In skin, environmental factors, for example, ultraviolet radiation (UVR), can accelerate the effects of aging such as decline in barrier function and subsequent loss of hydration. Water homeostasis is vital for all cellular functions and it is known that organic osmolyte transport is critical to this process. Therefore, we hypothesized that as we age, these tightly controlled physiological mechanisms become disrupted, possibly due to loss of transporter expression. We investigated this in vivo, using human skin samples from photoprotected and photoexposed sites of young and aged volunteers. We show a reduction in keratinocyte cell size with age and a downregulation of osmolyte transporters SMIT and TAUT with both chronic and acute UVR exposure. Single-cell live imaging demonstrated that aged keratinocytes lack efficient cell volume recovery mechanisms possessed by young keratinocytes following physiological stress. However, addition of exogenous taurine significantly rescued cell volume; this was corroborated by a reduction in TAUT mRNA and protein in aged, as compared to young, keratinocytes. Collectively, these novel data demonstrate that human epidermal keratinocytes possess osmolyte-mediated cell volume regulatory mechanisms, which may be compromised in aging. Therefore, this suggests that organic osmolytes-especially taurine-play a critical role in cutaneous age-related xerosis and highlights a fundamental mechanism, vital to our understanding of the pathophysiology of skin aging.

| S-EPMC6974728 | 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