Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigation of the interaction between patulin and human serum albumin by a spectroscopic method, atomic force microscopy, and molecular modeling.

ABSTRACT: The interaction of patulin with human serum albumin (HSA) was studied in vitro under normal physiological conditions. The study was performed using fluorescence, ultraviolet-visible spectroscopy (UV-Vis), circular dichroism (CD), atomic force microscopy (AFM), and molecular modeling techniques. The quenching mechanism was investigated using the association constants, the number of binding sites, and basic thermodynamic parameters. A dynamic quenching mechanism occurred between HSA and patulin, and the binding constants (K) were 2.60 × 10(4), 4.59 × 10(4), and 7.01 × 10(4)?M(-1) at 288, 300, and 310?K, respectively. Based on fluorescence resonance energy transfer, the distance between the HSA and patulin was determined to be 2.847?nm. The ?G (0), ?H (0), and ?S (0) values across various temperatures indicated that hydrophobic interaction was the predominant binding force. The UV-Vis and CD results confirmed that the secondary structure of HSA was altered in the presence of patulin. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with patulin. In addition, molecular modeling showed that the patulin-HSA complex was stabilized by hydrophobic and hydrogen bond forces. The study results suggested that a weak intermolecular interaction occurred between patulin and HSA. Overall, the results are potentially useful for elucidating the toxigenicity of patulin when it is combined with the biomolecular function effect, transmembrane transport, toxicological, testing and other experiments.

SUBMITTER: Yuqin L

PROVIDER: S-EPMC4119689 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Investigating the Effect of Tyrosine Kinase Inhibitors on the Interaction between Human Serum Albumin by Atomic Force Microscopy.

Project description:It is important for elucidating the regulation mechanism of life activities, as well as for the prevention, diagnosis, and drug design of diseases, to study protein-protein interactions (PPIs). Here, we investigated the interactions of human serum albumin (HSA) in the presence of tyrosine kinase inhibitors (TKIs: imatinib, nilotinib, dasatinib, bosutinib, and ponatinib) using atomic force microscopy (AFM). The distribution of rupture events including the specific interaction force Fi and the non-specific interaction force F0 between HSA pairs was analyzed. Based on the force measurements, Fi and F0 between HSA pairs in the control experiment were calculated to be 47 ± 1.5 and 116.1 ± 1.3 pN. However, Fi was significantly decreased in TKIs, while F0 was slightly decreased. By measuring the rupture forces at various loading rates and according to the Bell equation, the kinetic parameters of the complexes were investigated in greater detail. Molecular docking was used as a complementary means by which to explore the force of this effect. The whole measurements indicated that TKIs influenced PPIs in a variety of ways, among which hydrogen bonding and hydrophobic interactions were the most important. In conclusion, these outcomes give us a better insight into the mechanisms of PPIs when there are exogenous compounds present as well as in different liquid environments.

| S-EPMC9221072 | biostudies-literature

Closed-loop atomic force microscopy-infrared spectroscopic imaging for nanoscale molecular characterization.

Project description:Atomic force microscopy-infrared (AFM-IR) spectroscopic imaging offers non-perturbative, molecular contrast for nanoscale characterization. The need to mitigate measurement artifacts and enhance sensitivity, however, requires narrowly-defined and strict sample preparation protocols. This limits reliable and facile characterization; for example, when using common substrates such as Silicon or glass. Here, we demonstrate a closed-loop (CL) piezo controller design for responsivity-corrected AFM-IR imaging. Instead of the usual mode of recording cantilever deflection driven by sample expansion, the principle of our approach is to maintain a zero amplitude harmonic cantilever deflection by CL control of a subsample piezo. We show that the piezo voltage used to maintain a null deflection provides a reliable measure of the local IR absorption with significantly reduced noise. A complete analytical description of the CL operation and characterization of the controller for achieving robust performance are presented. Accurate measurement of IR absorption of nanothin PMMA films on glass and Silicon validates the robust capability of CL AFM-IR in routine mapping of nanoscale molecular information.

| S-EPMC7320136 | biostudies-literature

Easy and direct method for calibrating atomic force microscopy lateral force measurements.

Project description:We have designed and tested a new, inexpensive, easy-to-make and easy-to-use calibration standard for atomic force microscopy (AFM) lateral force measurements. This new standard simply consists of a small glass fiber of known dimensions and Young's modulus, which is fixed at one end to a substrate and which can be bent laterally with the AFM tip at the other end. This standard has equal or less error than the commonly used method of using beam mechanics to determine a cantilever's lateral force constant. It is transferable, thus providing a universal tool for comparing the calibrations of different instruments. It does not require knowledge of the cantilever dimensions and composition or its tip height. This standard also allows direct conversion of the photodiode signal to force and, thus, circumvents the requirement for a sensor response (sensitivity) measurement.

| S-EPMC3018784 | biostudies-literature

Quantifying Nanoparticle Layer Topography: Theoretical Modeling and Atomic Force Microscopy Investigations.

Project description:A comprehensive method consisting of theoretical modeling and experimental atomic force microscopy (AFM) measurements was developed for the quantitative analysis of nanoparticle layer topography. Analytical results were derived for particles of various shapes such as cylinders (rods), disks, ellipsoids, hemispheres (caps), etc. It was shown that for all particles, their root-mean-square (rms) parameter exhibited a maximum at the coverage about 0.5, whereas the skewness was a monotonically decreasing function of the coverage. This enabled a facile determination of the particle coverage in the layer, even if the shape and size were not known. The validity of the analytical results was confirmed by computer modeling and experimental data acquired by AFM measurements for polymer nanoparticle deposition on mica and silica. The topographical analysis developed in this work can be exploited for a quantitative characterization of self-assembled layers of nano- and bioparticles, e.g., carbon nanotubes, silica and noble metal particles, DNA fragments, proteins, vesicles, viruses, and bacteria at solid surfaces. The acquired results also enabled a proper calibration, in particular the determination of the measurement precision, of various electron and scanning probe microscopies, such as AFM.

| S-EPMC10601541 | biostudies-literature

Localization atomic force microscopy.

Project description:Understanding structural dynamics of biomolecules at the single-molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there are few techniques that can capture dynamics at the sub-nanometre scale and in physiologically relevant conditions. Atomic force microscopy (AFM)1 has the advantage of analysing unlabelled single molecules in physiological buffer and at ambient temperature and pressure, but its resolution limits the assessment of conformational details of biomolecules2. Here we present localization AFM (LAFM), a technique developed to overcome current resolution limitations. By applying localization image reconstruction algorithms3 to peak positions in high-speed AFM and conventional AFM data, we increase the resolution beyond the limits set by the tip radius, and resolve single amino acid residues on soft protein surfaces in native and dynamic conditions. LAFM enables the calculation of high-resolution maps from either images of many molecules or many images of a single molecule acquired over time, facilitating single-molecule structural analysis. LAFM is a post-acquisition image reconstruction method that can be applied to any biomolecular AFM dataset.

| S-EPMC8697813 | biostudies-literature

Interaction of virstatin with human serum albumin: spectroscopic analysis and molecular modeling.

Project description:Virstatin is a small molecule that inhibits Vibrio cholerae virulence regulation, the causative agent for cholera. Here we report the interaction of virstatin with human serum albumin (HSA) using various biophysical methods. The drug binding was monitored using different isomeric forms of HSA (N form ?pH 7.2, B form ?pH 9.0 and F form ?pH 3.5) by absorption and fluorescence spectroscopy. There is a considerable quenching of the intrinsic fluorescence of HSA on binding the drug. The distance (r) between donor (Trp214 in HSA) and acceptor (virstatin), obtained from Forster-type fluorescence resonance energy transfer (FRET), was found to be 3.05 nm. The ITC data revealed that the binding was an enthalpy-driven process and the binding constants K(a) for N and B isomers were found to be 6.09×10(5 )M(-1) and 4.47×10(5) M(-1), respectively. The conformational changes of HSA due to the interaction with the drug were investigated from circular dichroism (CD) and Fourier Transform Infrared (FTIR) spectroscopy. For 1:1 molar ratio of the protein and the drug the far-UV CD spectra showed an increase in ?- helicity for all the conformers of HSA, and the protein is stabilized against urea and thermal unfolding. Molecular docking studies revealed possible residues involved in the protein-drug interaction and indicated that virstatin binds to Site I (subdomain IIA), also known as the warfarin binding site.

| S-EPMC3359307 | biostudies-literature

Modeling viscoelasticity through spring-dashpot models in intermittent-contact atomic force microscopy.

Project description:We examine different approaches to model viscoelasticity within atomic force microscopy (AFM) simulation. Our study ranges from very simple linear spring-dashpot models to more sophisticated nonlinear systems that are able to reproduce fundamental properties of viscoelastic surfaces, including creep, stress relaxation and the presence of multiple relaxation times. Some of the models examined have been previously used in AFM simulation, but their applicability to different situations has not yet been examined in detail. The behavior of each model is analyzed here in terms of force-distance curves, dissipated energy and any inherent unphysical artifacts. We focus in this paper on single-eigenmode tip-sample impacts, but the models and results can also be useful in the context of multifrequency AFM, in which the tip trajectories are very complex and there is a wider range of sample deformation frequencies (descriptions of tip-sample model behaviors in the context of multifrequency AFM require detailed studies and are beyond the scope of this work).

| S-EPMC4273292 | biostudies-literature

Elucidating the Geometric Substitution of Petroporphyrins by Spectroscopic Analysis and Atomic Force Microscopy Molecular Imaging.

Project description:Determination of the molecular structures of petroporphyrins has been crucial to understand the diagenetic pathways and maturation of petroleum. However, these studies have been hampered by their structural complexity and the challenges associated with their isolation. In comparison to the skeletal macrocyclic structures, much less is known about the substitutions, which are more sensitive to the maturation and diagenesis pathways. While these isolated vanadyl petroporphyrins largely consist of etioporphyrin and deoxophylloerythroetioporphyrin as expected, surprisingly, we find evidence that one or a few β hydrogens are present in petroporphyrins of low carbon numbers using a combination of ultraviolet-visible spectroscopy, Fourier transform ion cyclotron resonance mass spectrometry, and non-contact atomic force microscopy. Petroporphyrins with β hydrogens were not anticipated on the basis of their biological precursors. The data support dealkylation under catagenesis but not transalkylation or random alkylation of the β and meso positions, despite the fact that more complex porphyrin structures are formed.

| S-EPMC6647966 | biostudies-literature

Electrostatic Discovery Atomic Force Microscopy.

Project description:While offering high resolution atomic and electronic structure, scanning probe microscopy techniques have found greater challenges in providing reliable electrostatic characterization on the same scale. In this work, we offer electrostatic discovery atomic force microscopy, a machine learning based method which provides immediate maps of the electrostatic potential directly from atomic force microscopy images with functionalized tips. We apply this to characterize the electrostatic properties of a variety of molecular systems and compare directly to reference simulations, demonstrating good agreement. This approach offers reliable atomic scale electrostatic maps on any system with minimal computational overhead.

| S-EPMC8793147 | biostudies-literature

Multi-spectroscopic investigation of the binding interaction of fosfomycin with bovine serum albumin.

Project description:The interaction between fosfomycin (FOS) and bovine serum albumin (BSA) has been investigated effectively by multi-spectroscopic techniques under physiological pH 7.4. FOS quenched the intrinsic fluorescence of BSA via static quenching. The number of binding sites n and observed binding constant KA were measured by the fluorescence quenching method. The thermodynamic parameters ?G0, ?H0 and ?S0 were calculated at different temperatures according to the van't Hoff equation. The site of binding of FOS in the protein was proposed to be Sudlow's site I based on displacement experiments using site markers viz. warfarin, ibuprofen and digitoxin. The distance r between the donor (BSA) and acceptor (FOS) molecules was obtained according to the Förster theory. The effect of FOS on the conformation of BSA was analyzed using synchronous fluorescence spectra (SFS), circular dichroism (CD) and 3D fluorescence spectra. A molecular modeling study further confirmed the binding mode obtained by the experimental studies.

| S-EPMC5762212 | 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