Browse
Submit Data
Databases
API
Help

Dataset Information

35 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Interfacial Modeling of Fibrinogen Adsorption onto LiNbO₃ Single Crystal-Single Domain Surfaces.

ABSTRACT: For the development of next-generation protein-based biosensor surfaces, it is important to understand how functional proteins, such as fibrinogen (FBG), interact with polar substrate surfaces in order to prepare highly sensitive points of medical care diagnostics. FBG, which is a fibrous protein with an extracellular matrix, has both positively and negatively charged regions on its 3-dimensional surface, which makes interpreting how it effectively binds to polarized surfaces challenging. In this study, single-crystal LiNbO₃ (LNO) substrates that have surface charges were used to investigate the adsorption of FBG protruding polar fragments on the positively and negatively charged LNO surfaces. We performed a combination of experiments and multi-scale molecular modeling to understand the binding of FBG in vacuum and water-solvated surfaces of LNO. XPS measurements showed that the FBG adsorption on LNO increased with increment in solution concentration on surfaces independent of charges. Multi-scale molecular modeling employing Quantum Mechanics, Monte Carlo, and Molecular Mechanics addressed the phenomenon of FBG fragment bonding on LNO surfaces. The binding simulation validated the experimental observation using zeta potential measurements which showed presence of solvated medium influenced the adsorption phenomenon due to the negative surface potential.

SUBMITTER: Cross JS

PROVIDER: S-EPMC8199120 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Albumin (BSA) adsorption onto graphite stepped surfaces.

Project description:Nanomaterials are good candidates for the design of novel components with biomedical applications. For example, nano-patterned substrates may be used to immobilize protein molecules in order to integrate them in biosensing units. Here, we perform long MD simulations (up to 200 ns) using an explicit solvent and physiological ion concentrations to characterize the adsorption of bovine serum albumin (BSA) onto a nano-patterned graphite substrate. We have studied the effect of the orientation and step size on the protein adsorption and final conformation. Our results show that the protein is stable, with small changes in the protein secondary structure that are confined to the contact area and reveal the influence of nano-structuring on the spontaneous adsorption, protein-surface binding energies, and protein mobility. Although van der Waals (vdW) interactions play a dominant role, our simulations reveal the important role played by the hydrophobic lipid-binding sites of the BSA molecule in the adsorption process. The complex structure of these sites, that incorporate residues with different hydrophobic character, and their flexibility are crucial to understand the influence of the ion concentration and protein orientation in the different steps of the adsorption process. Our study provides useful information for the molecular engineering of components that require the immobilization of biomolecules and the preservation of their biological activity.

| S-EPMC5457296 | biostudies-literature

Crystal alignment of caffeine deposited onto single crystal surfaces <i>via</i> hot-wall epitaxy.

Project description:Defined crystal growth is highly demanded for technological applications but also fundamental research. Within this work, the crystal growth of the asymmetric molecule caffeine was studied on single crystalline surfaces of muscovite mica, sodium chloride and potassium chloride. While elongated needle-like crystals grow on muscovite mica and sodium chloride, smaller individual "bird-like" structures were observed on potassium chloride. Depending on the surface type and temperature, the disk-shaped caffeine molecules prefer either an edge-on or flat-on orientation with respect to the surface, but in each case, a defined crystallographic relation between the surface and caffeine crystallites was determined by using the X-ray pole figure technique. On muscovite mica and sodium chloride, needle-like crystallites with edge-on oriented molecules aligned mainly with the unit cell c-axis (which coincides with the long needle axis) along the [1-10]mica, [100]mica, [110]mica and [110]NaCl, [1-10]NaCl directions, respectively. Crystals consisting of flat-on oriented molecules on KCl showed also defined alignments with respect to the substrate, but due to the altered molecule-substrate contact, the b-axis aligned along [110]KCl and [1-10]KCl. Growth at elevated temperatures enabled changes in the crystal growth whereby more defined structures formed on NaCl. On KCl, the bird-like structures remained very similar, while caffeine on the mica surface at elevated temperatures resulted in even additional texture forming with the caffeine molecules now also favoring a flat-on orientation with respect to the surface. The systematic variation of various system parameters demonstrates how sensitive the growth behavior of caffeine on this variety of substrates is.

| S-EPMC5471919 | biostudies-literature

Using a fluorescence quenching method to detect DNA adsorption onto single-walled carbon nanotube surfaces.

Project description:Surface modification of single-walled carbon nanotubes (SWNTs) with DNA molecules has attracted much attention in recent years to increase SWNT solubility and make various SWNT-based nanobiodevices. Therefore, there is a critical need to quantify the interaction between DNA molecules and SWNT surfaces, particularly the intermediate structures during DNA adsorption. In this study, we demonstrate the ability to detect the adsorption of DNA oligomers on SWNT surfaces by fluorescence spectroscopy. Fluorescein-labelled, 30mer, thymine oligonucleotides (F-T30) were employed as a fluorescent probe to study the interaction of DNA with SWNTs. A clear quenching effect was observed when F-T30 was adsorbed onto SWNT surfaces. Using this method, the amount of DNA adsorbed onto the SWNT surfaces was measured under different sonication conditions to correlate adsorption efficiency with sonication strength and duration. When a bath-type sonicator was used, mild adsorption of F-T30 on SWNT surfaces was observed. Furthermore, a two-step adsorption was observed in this condition. In contrast, we observed rapid adsorption of F-T30 to SWNT surfaces at the higher sonication amplitude (60% maximal) using a probe-type sonicator, while only slight adsorption of DNA molecules was observed at the lower amplitude (20% maximal). Our data revealed that the quenching effect can be used to evaluate DNA adsorption onto SWNT surfaces. In addition, atomic force microscopy (AFM) and photoacoustic spectroscopy (PAS) were conducted to provide complementary information on the DNA-SWNT nanoconjugates.

| S-EPMC5714673 | biostudies-literature

Albumin adsorption onto surfaces of urine collection and analysis containers.

Project description:BackgroundAdsorption of albumin onto urine collection and analysis containers may cause falsely low concentrations.MethodsWe added (125)I-labeled human serum albumin to urine and to phosphate buffered solutions, incubated them with 22 plastic container materials and measured adsorption by liquid scintillation counting.ResultsAdsorption of urine albumin (UA) at 5-6 mg/l was <0.9%; and at 90 mg/l was <0.4%. Adsorption was generally less at pH8 than pH5 but only 3 cases had p<0.05. Adsorption from 11 unaltered urine samples with albumin 5-333 mg/l was <0.8%. Albumin adsorption for the material with greatest binding was extrapolated to the surface areas of 100 ml and 2l collection containers, and to instrument sample cups and showed <1% change in concentration at 5 mg/l and <0.5% change at 20 mg/l or higher concentrations. Adsorption of albumin from phosphate buffered solutions (2-28%) was larger than that from urine.ConclusionsAlbumin adsorption differed among urine samples and plastic materials, but the total influence of adsorption was <1% for all materials and urine samples tested. Adsorption of albumin from phosphate buffered solutions was larger than that from urine and could be a limitation for preparations used as calibrators.

| S-EPMC5708857 | biostudies-literature

Adsorption of Fibrinogen on Silica Surfaces-The Effect of Attached Nanoparticles.

Project description:When a biomaterial is inserted into the body, proteins rapidly adsorb onto its surface, creating a conditioning protein film that functions as a link between the implant and adhering cells. Depending on the nano-roughness of the surface, proteins will adsorb in different amounts, with different conformations and orientations, possibly affecting the subsequent attachment of cells to the surface. Thus, modifications of the surface nanotopography of an implant may prevent biomaterial-associated infections. Fibrinogen is of particular importance since it contains adhesion epitopes that are recognized by both eukaryotic and prokaryotic cells, and can therefore influence the adhesion of bacteria. The aim of this study was to model adsorption of fibrinogen to smooth or nanostructured silica surfaces in an attempt to further understand how surface nanotopography may affect the orientation of the adsorbed fibrinogen molecule. We used a coarse-grained model, where the main body of fibrinogen (visible in the crystal structure) was modeled as rigid and the flexible ? C-chains (not visible in the crystal structure) were modeled as completely disordered. We found that the elongated fibrinogen molecule preferably adsorbs in such a way that it protrudes further into solution on a nanostructured surface compared to a flat one. This implicates that the orientation on the flat surface increases its bio-availability.

| S-EPMC7175343 | biostudies-literature

Adsorption of ice-binding proteins onto whole ice crystal surfaces does not necessarily confer a high thermal hysteresis activity.

Project description:Many psychrophilic microorganisms synthesize ice-binding proteins (IBPs) to survive the cold. The functions of IBPs are evaluated by the effect of the proteins on the nonequilibrium water freezing-point depression, which is called "thermal hysteresis (TH)", and the inhibitory effect of the proteins on the growth of larger ice crystals, which is called "ice recrystallization inhibition (IRI)". To obtain mechanical insight into the two activities, we developed a modified method of ice affinity purification and extracted two new IBP isoforms from Psychromyces glacialis, an Arctic glacier fungus. One isoform was found to be an approximately 25 kDa protein (PsgIBP_S), while the other is a 28 kDa larger protein (PsgIBP_L) that forms an intermolecular dimer. Their TH activities were less than 1 °C at millimolar concentrations, implying that both isoforms are moderately active but not hyperactive IBP species. It further appeared that both isoforms exhibit high IRI activity even at submicromolar concentrations. Furthermore, the isoforms can bind to the whole surface of a hemispherical single ice crystal, although such ice-binding was generally observed for hyperactive IBP species. These results suggest that the binding ability of IBPs to whole ice crystal surfaces is deficient for hyperactivity but is crucial for significant IRI activity.

| S-EPMC9474881 | biostudies-literature

Adsorption of Malathion onto Copper and Iron Surfaces Relevant to Water Infrastructure.

Project description:This study investigated the adsorption of malathion to copper and iron surfaces including microspheres and pipe specimens similar to those in drinking water infrastructure. The solid phase concentration of malathion on the virgin and used copper pipe specimens was generally between 0.2 - 1 mg/g. The adsorption capacity for copper and iron microspheres were greater than those of the pipe specimens because of their higher surface area-to-volume ratios. Copper materials adsorbed more malathion than comparable iron materials. XPS analysis of copper and iron surfaces revealed peaks at 164 eV (S 2p) and 135 eV (P 2p), which suggests that malathion chemically bonded to the surfaces of the specimens. Metal oxides likely formed stable bonds with phosphorus through pi conjugation. These findings are the first to show that malathion can chemically adhere to copper and iron pipe materials. This insight is critical for understanding the decontamination strategies needed for water networks.

| S-EPMC6198671 | biostudies-literature

Adsorption Dynamics of Redox Active Species onto Polarized Surfaces of Sensitized NiO.

Project description:Mesoporous NiO films were deposited by means of a screen printing technique onto fluorine-doped tin oxide transparent electrodes and consequently sensitized with Erythrosin B (EryB) dye. The obtained colored NiO material was used as a working electrode in a three-electrode cell to study the evolution of the triple semiconductor/dye/electrolyte interface upon electrochemical polarization in dark conditions. The electrolyte was a solution of I3 -/I- in acetonitrile, with the redox couple representing the typical redox shuttle of dye-sensitized solar cells (DSCs). The adopted electrochemical conditions were devised in order to simulate the actual electrical environment of the NiO/dye photocathode in a light-soaked DSC. The use of a benchmark sensitizer EryB and of the most widely used redox mediator I3 -/I- is particularly meaningful for the study of the adsorption dynamics and the determination of possible degradative phenomena on the basis of the behavior of numerous analogue systems. Therefore, for the first time, the evolution of the NiO/EryB/I3 -/I- multiple interface was investigated combining the electrochemical characterization with ex situ spectroscopic analysis by means of X-ray photoelectron spectroscopy. The resulting picture shows that EryB in the immobilized state promotes the redox processes based on the I3 -/I- couple. Moreover, the EryB sensitizer inhibits the phenomena of recombination between the metal oxide semiconductor and the redox couple.

| S-EPMC6648089 | biostudies-literature

Role of the dispersion force in modeling the interfacial properties of molecule-metal interfaces: adsorption of thiophene on copper surfaces.

Project description:We present density functional theory calculations of the geometry, adsorption energy and electronic structure of thiophene adsorbed on Cu(111), Cu(110) and Cu(100) surfaces. Our calculations employ dispersion corrections and self-consistent van der Waals density functionals (vdW-DFs). In terms of speed and accuracy, we find that the dispersion-energy-corrected Revised Perdue-Burke-Enzerhof (RPBE) functional is the "best balanced" method for predicting structural and energetic properties, while vdW-DF is also highly accurate if a proper exchange functional is used. Discrepancies between theory and experiment in molecular geometry can be solved by considering x-ray generated core-holes. However, the discrepancy concerning the adsorption site for thiophene/Cu(100) remains unresolved and requires both further experiments and deeper theoretical analysis. For all the interfaces, the PBE functional reveals a covalent bonding picture which the inclusion of dispersive contributions does not change to a vdW one. Our results provide a comprehensive understanding of the role of dispersive forces in modelling molecule-metal interfaces.

| S-EPMC4030267 | biostudies-other

Density functional theory modeling of chromate adsorption onto ferrihydrite nanoparticles.

Project description:Density functional theory (DFT) calculations were performed on a model of a ferrihydrite nanoparticle interacting with chromate ([Formula: see text]) in water. Two configurations each of monodentate and bidentate adsorbed chromate as well as an outer-sphere and a dissolved bichromate ([Formula: see text]) were simulated. In addition to the 3-D periodic planewave DFT models, molecular clusters were extracted from the energy-minimized structures. Calculated interatomic distances from the periodic and cluster models compare favorably with Extended X-ray Absorption Fine Structure spectroscopy values, with larger discrepancies seen for the clusters due to over-relaxation of the model substrate. Relative potential energies were derived from the periodic models and Gibbs free energies from the cluster models. A key result is that the bidentate binuclear configuration is the lowest in potential energy in the periodic models followed by the outer-sphere complex. This result is consistent with observations of the predominance of bidentate chromate adsorption on ferrihydrite under conditions of high surface coverage (Johnston Environ Sci Technol 46:5851-5858, 2012). Cluster models were also used to perform frequency analyses for comparison with observed ATR FTIR spectra. Calculated frequencies on monodentate, bidentate binuclear, and outer-sphere complexes each have infrared (IR)-active modes consistent with experiment. Inconsistencies between the thermodynamic predictions and the IR-frequency analysis suggest that the 3-D periodic models are not capturing key components of the system that influence the adsorption equilibria under varying conditions of pH, ionic strength and electrolyte composition. Model equilibration via molecular dynamics (MD) simulations is necessary to escape metastable states created during DFT energy minimizations based on the initial classical force field MD-derived starting configurations.

| S-EPMC5832661 | biostudies-literature