Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mineral Surface Chemistry and Nanoparticle-aggregation Control Membrane Self-Assembly.

ABSTRACT: The self-assembly of lipid bilayer membranes to enclose functional biomolecules, thus defining a "protocell," was a seminal moment in the emergence of life on Earth and likely occurred at the micro-environment of the mineral-water interface. Mineral-lipid interactions are also relevant in biomedical, industrial and technological processes. Yet, no structure-activity relationships (SARs) have been identified to predict lipid self-assembly at mineral surfaces. Here we examined the influence of minerals on the self-assembly and survival of vesicles composed of single chain amphiphiles as model protocell membranes. The apparent critical vesicle concentration (CVC) increased in the presence of positively-charged nanoparticulate minerals at high loadings (mg/mL) suggesting unfavorable membrane self-assembly in such situations. Above the CVC, initial vesicle formation rates were faster in the presence of minerals. Rates were correlated with the mineral's isoelectric point (IEP) and reactive surface area. The IEP depends on the crystal structure, chemical composition and surface hydration. Thus, membrane self-assembly showed rational dependence on fundamental mineral properties. Once formed, membrane permeability (integrity) was unaffected by minerals. Suggesting that, protocells could have survived on rock surfaces. These SARs may help predict the formation and survival of protocell membranes on early Earth and other rocky planets, and amphiphile-mineral interactions in diverse other phenomena.

SUBMITTER: Sahai N

PROVIDER: S-EPMC5339912 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Mineral surface chemistry control for origin of prebiotic peptides.

Project description:Some seventy years ago, John Desmond Bernal proposed a role for clays in the origin of life. While much research has since been dedicated to the study of silicate clays, layered double hydroxides, believed to be common on the early Earth, have received only limited attention. Here we examine the role that layered hydroxides could have played in prebiotic peptide formation. We demonstrate how these minerals can concentrate, align and act as adsorption templates for amino acids, and during wetting-drying cycles, promote peptide bond formation. This enables us to propose a testable mechanism for the growth of peptides at layered double hydroxide interfaces in an early Earth environment. Our results provide insights into the potential role of mineral surfaces in mimicking aspects of biochemical reaction pathways.

| S-EPMC5725419 | biostudies-literature

Gold Nanoparticle Self-Aggregation on Surface with 1,6-Hexanedithiol Functionalization.

Project description:Here we study the morphology and the optical properties of assemblies made of small (17 nm) gold nanoparticles (AuNPs) directly on silicon wafers coated with (3-aminopropyl)trimethoxysilane (APTES). We employed aliphatic 1,6-hexanedithiol (HDT) molecules to cross-link AuNPs during a two-stage precipitation procedure. The first immersion of the wafer in AuNP colloidal solution led mainly to the attachment of single particles with few inclusions of dimers and small aggregates. After the functionalization of precipitated NPs with HDT and after the second immersion in the colloidal solution of AuNP, we detected a sharp rise in the number of aggregates compared to single AuNPs and their dimers. The lateral size of the aggregates was about 100 nm, while some of them were larger than 1?m. We propose that the uncompensated dipole moment of the small aggregates appeared after the first precipitation and acts further as the driving force accelerating their further growth on the surface during the second precipitation. By having such inhomogeneous surface coating, the X-ray reciprocal space maps and modulation polarimetry showed well-distinguished signals from the single AuNPs and their dimers. From these observations, we concluded that the contribution from aggregated AuNPs does not hamper the detection and investigation of plasmonic effects for AuNP dimers. Meantime, using unpolarized and polarized light spectroscopy, the difference in the optical signals between the dimers, being formed because of self-aggregation and the one being cross-linked by means of HDT, was not detected.

| S-EPMC7153467 | biostudies-literature

Silver Nanoparticle Surface Enabled Self-Assembly of Organic Dye Molecules.

Project description:Fluorescence titration of methylene blue, rhodamine B and rhodamine 6G (R6G) by silver nanoparticle (AgNP) all resulted in an initial steep quenching curve followed with a sharp turn and a much flatter quenching curve. At the turn, there are about 200,000 dye molecules per a single AgNP, signifying self-assembly of approximately 36-layers of dye molecules on the surface of the AgNP to form a micelle-like structure. These fluorescence-quenching curves fit to a mathematical model with an exponential term due to molecular self-assembly on AgNP surface, or we termed it "self-assembly shielding effect", and a Stern-Volmer term (nanoparticle surface enhanced quenching). Such a "super-quenching" by AgNP can only be attributed to "pre-concentration" of the dye molecules on the nanoparticle surface that yields the formation of micelle-like self-assembly, resulting in great fluorescence quenching. Overall, the fluorescence quenching titration reveals three different types of interactions of dye molecules on AgNP surface: 1) self-assembly (methylene blue, rhodamine B and R6G), 2) absorption/tight interaction (tryptamine and fluorescein), and 3) loose interaction (eosin Y). We attribute the formation of micelle-like self-assembly of these three dye molecules on AgNP to their positive charge, possession of nitrogen atoms, and with relatively large and flat aromatic moieties.

| S-EPMC6720720 | biostudies-literature

Single-residue physicochemical characteristics kinetically partition membrane protein self-assembly and aggregation.

Project description:Ninety-five percent of all transmembrane proteins exist in kinetically trapped aggregation-prone states that have been directly linked to neurodegenerative diseases. Interestingly, the primary sequence almost invariably avoids off-pathway aggregate formation, by folding reliably into its native, thermodynamically stabilized structure. However, with the rising incidence of protein aggregation diseases, it is now important to understand the underlying mechanism(s) of membrane protein aggregation. Micromolecular physicochemical and biochemical alterations in the primary sequence that trigger the formation of macromolecular cross-β aggregates can be measured only through combinatorial spectroscopic experiments. Here, we developed spectroscopic thermal perturbation with 117 experimental variables to assess how subtle protein sequence variations drive the molecular transition of the folded protein to oligomeric aggregates. Using the Yersinia pestis outer transmembrane β-barrel Ail as a model, we delineated how a single-residue substitution that alters the membrane-anchoring ability of Ail significantly contributes to the kinetic component of Ail stability. We additionally observed a stabilizing role for interface aliphatics, and that interface aromatics physicochemically contribute to Ail self-assembly and aggregation. Moreover, our method identified the formation of structured oligomeric intermediates during Ail aggregation. We show that the self-aggregation tendency of Ail is offset by the evolution of a thermodynamically compromised primary sequence that balances folding, stability, and oligomerization. Our approach provides critical information on how subtle changes in protein primary sequence trigger cross-β fibril formation, with insights that have direct implications for deducing the molecular progression of neurodegeneration and amyloidogenesis in humans.

| S-EPMC6996891 | biostudies-literature

Stability of radical-functionalized gold surfaces by self-assembly and on-surface chemistry.

Project description:We have investigated the radical functionalization of gold surfaces with a derivative of the perchlorotriphenylmethyl (PTM) radical using two methods: by chemisorption from the radical solution and by on-surface chemical derivation from a precursor. We have investigated the obtained self-assembled monolayers by photon-energy dependent X-ray photoelectron spectroscopy. Our results show that the molecules were successfully anchored on the surfaces. We have used a robust method that can be applied to a variety of materials to assess the stability of the functionalized interface. The monolayers are characterized by air and X-ray beam stability unprecedented for films of organic radicals. Over very long X-ray beam exposure we observed a dynamic nature of the radical-Au complex. The results clearly indicate that (mono)layers of PTM radical derivatives have the necessary stability to withstand device applications.

| S-EPMC8163401 | biostudies-literature

Plug-based microfluidics with defined surface chemistry to miniaturize and control aggregation of amyloidogenic peptides.

Project description:Small with control: For miniaturization of protein aggregation experiments the interfacial chemistry must be controlled to avoid protein aggregation caused by interfacial adsorption. Plug-based microfluidics with defined surface chemistry (see schematic picture) can then be used to perform hundreds of aggregation experiments with volume-limited samples, such as cerebrospinal fluid from mice.

| S-EPMC2675571 | biostudies-literature

Tuning of nanoparticle biological functionality through controlled surface chemistry and characterisation at the bioconjugated nanoparticle surface.

Project description:We have used a silica - PEG based bionanoconjugate synthetic scheme to study the subtle connection between cell receptor specific recognition and architecture of surface functionalization chemistry. Extensive physicochemical characterization of the grafted architecture is capable of capturing significant levels of detail of both the linker and grafted organization, allowing for improved reproducibility and ultimately insight into biological functionality. Our data suggest that scaffold details, propagating PEG layer architecture effects, determine not only the rate of uptake of conjugated nanoparticles into cells but also, more significantly, the specificity of pathways via which uptake occurs.

| S-EPMC4664868 | biostudies-literature

Low-Dose Silver Nanoparticle Surface Chemistry and Temporal Effects on Gene Expression in HepG2 Cells

Project description:We examined effects of surface-coating (BPEI, CIT, PEG) of silver nanoparticles and time (6h, 12h, 24h) on gene expression in human liver cancer cells (HepG2)

2020-06-01 | GSE143717 | GEO

Nanoscale Control of Amyloid Self-Assembly Using Protein Phase Transfer by Host-Guest Chemistry.

Project description:Amyloid fibrils have recently been highlighted for their diverse applications as functional nanomaterials in modern chemistry. However, tight control to obtain a targeted fibril length with low heterogeneity has not been achieved because of the complicated nature of amyloid fibrillation. Herein, we demonstrate that fibril assemblies can be homogeneously manipulated with desired lengths from ~40?nm to ~10??m by a phase transfer of amyloid proteins based on host-guest chemistry. We suggest that host-guest interactions with cucurbit[6]uril induce a phase transfer of amyloid proteins (human insulin, human islet amyloid polypeptide, hen egg lysozyme, and amyloid-? 1-40 & 1-42) from the soluble state to insoluble state when the amount of cucurbit[6]uril exceeds its solubility limit in solution. The phase transfer of the proteins kinetically delays the nucleation of amyloid proteins, while the nuclei formed in the early stage are homogeneously assembled to fibrils. Consequently, supramolecular assemblies of amyloid proteins with heterogeneous kinetics can be controlled by protein phase transfer based on host-guest interactions.

| S-EPMC5516018 | biostudies-literature

Tuning the Surface Charge of Self-Assembled Polydiacetylene Vesicles to Control Aggregation and Cell Binding.

Project description:Polydiacetylene vesicles of various compositions were assembled using a two-part mixture of 10,12-pentacosadiynoic acid (PCDA) and ethylenedioxy-bis-ethylamine (EDEA)-labeled PCDA in order to control surface charge and stability within a desired pH range. Investigation of the interaction of the vesicles with mammalian cells as a function of surface charge was carried out and identified a clear correlation in cell-vesicle association and corresponding cell death for vesicles with positive surface charge. The binding behavior of the vesicles was found to be tunable by regulating the proportion of anionic PCDA relative to cationic PCDA-EDEA content within vesicles as to control the surface charge as a function of pH. Association of vesicles with cells thus depended on the corresponding charge of the vesicles and cell surface. The prospect of this work may serve as a step toward future vesicle designs to allow triggered uptake of vesicles locally within low pH tumor microenvironments.

| S-EPMC7598607 | 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