Browse
Submit Data
Databases
API
Help

Dataset Information

35 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Probing Bioelectronic Connections Using Streptavidin Molecules with Modified Valency.

ABSTRACT: As molecular electronic components, proteins are distinguished by a remarkably long electronic decay length (∼10 nm) together with high contact resistance and extreme sensitivity to the chemical details of the contact. As a consequence, the conductance of even a large bioelectronic assembly is largely controlled by the conductance of the contacts. Streptavidin is a versatile linker protein that can tether together biotinylated electrodes and biotinylated proteins but with an ambiguity about the contact geometry that arises from its four possible binding sites for biotin. Here, we use engineered streptavidin tetramers, selected to contain a defined ratio of active monomers to "dead" monomers so as to define the biotin binding sites. We find a strong dependence of conductance on the separation of the biotin molecules, consistent with a short-range tunneling interaction within the streptavidin and in contrast to the long-range transport observed inside larger proteins. Hexaglutamate tails label the active monomers, and the additional negative charge enhances conductance significantly. This effect is quantitatively accounted for by an electronic resonance in the protein conductance.

SUBMITTER: Zhang B

PROVIDER: S-EPMC8458255 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Bioelectronic measurement and feedback control of molecules in living cells.

Project description:We describe an electrochemical measurement technique that enables bioelectronic measurements of reporter proteins in living cells as an alternative to traditional optical fluorescence. Using electronically programmable microfluidics, the measurement is in turn used to control the concentration of an inducer input that regulates production of the protein from a genetic promoter. The resulting bioelectronic and microfluidic negative-feedback loop then serves to regulate the concentration of the protein in the cell. We show measurements wherein a user-programmable set-point precisely alters the protein concentration in the cell with feedback-loop parameters affecting the dynamics of the closed-loop response in a predictable fashion. Our work does not require expensive optical fluorescence measurement techniques that are prone to toxicity in chronic settings, sophisticated time-lapse microscopy, or bulky/expensive chemo-stat instrumentation for dynamic measurement and control of biomolecules in cells. Therefore, it may be useful in creating a: cheap, portable, chronic, dynamic, and precise all-electronic alternative for measurement and control of molecules in living cells.

| S-EPMC5624954 | biostudies-literature

Simple and rapid monitoring of doxorubicin using streptavidin-modified microparticle-based time-resolved fluorescence immunoassay.

Project description:Developing a simple analytical method suitable for therapeutic drug monitoring in a clinical setting is key to establishing guidelines on accurate dose administration and the advancement of precision medicine. We devised a simple rapid analytical method through the combination of streptavidin-modified microparticles and a time-resolved fluorescence immunoassay for therapeutic drug monitoring. The analytical performance of this method was investigated and validated using clinical samples. By determination of doxorubicin concentration, the proposed assay has shown a satisfactory linear range of detection (3.8-3000 ng mL-1) with a limit of detection of 3.8 ng mL-1 and an IC50 of 903.9 ng mL-1. The intra and inter-assay coefficients of variation were 4.12-5.72% and 5.48-6.91%, respectively, and the recovery was acceptable. The applicability of the proposed assay was assessed by comparing the determined results with those measured by LC-MS/MS, presenting a satisfactory correlation (R 2 = 0.9868). The proposed assay, which shows satisfactory analytical performance, has great potential for application in the field of TDM in the future.

| S-EPMC9080157 | biostudies-literature

Multivalent Benzamidine Molecules for Plasmin Inhibition: Effect of Valency and Linker Length.

Project description:There is an emerging interest in utilizing synthetic multivalent inhibitors that comprise of multiple inhibitor moieties linked on a common scaffold to achieve strong and selective enzyme inhibition. As multivalent inhibition is impacted by valency and linker length, in this study, we explore the effect of multivalent benzamidine inhibitors of varying valency and linker length on plasmin inhibition. Plasmin is an endogenous enzyme responsible for digesting fibrin present in blood clots. Monovalent plasmin(ogen) inhibitors are utilized clinically to treat hyperfibrinolysis-associated bleeding events. Benzamidine is a reversible inhibitor that binds to plasmin's active site. Herein, multivalent benzamidine inhibitors of varying valencies (mono-, bi- and tri-valent) and linker lengths (∼1-12 nm) were synthesized to systematically study their effect on plasmin inhibition. Inhibition assays were performed using a plasmin substrate (S-2251) to determine inhibition constants (Ki). Pentamidine (shortest bivalent) and Tri-AMB (shortest trivalent) were the strongest inhibitors with Ki values of 2.1±0.8 and 3.9±1.7 μM, respectively. Overall, increasing valency and decreasing linker length, increases effective local concentration of the inhibitor and therefore, resulted in stronger inhibition of plasmin via statistical rebinding. This study aids in the design of multivalent inhibitors that can achieve desired enzyme inhibition by means of modulating valency and linker length.

| S-EPMC9828467 | biostudies-literature

In Situ Probing of Photoinduced Hydrophilicity on Titania Surface Using Dye Molecules.

Project description:The titania film surface exhibits superhydrophilicity after UV irradiation due to its photocatalytic function. This is caused by a change in the density of the surface hydroxyl groups, which affects the surface charge density. Titania films were prepared to observe the change in the surface charge during UV irradiation. The amounts of some xanthene dyes adsorbed and deposited on the titania films after UV irradiation were evaluated as a function of the irradiation time. The increase in the adsorption and deposition amounts of the more negative dye versus the UV irradiation time was greater. These results indicated that the titania surface charge became more positive by the UV irradiation. It was reported that basic hydroxyl groups formed on the titania particle surface during the UV irradiation. The surface dissociates hydroxyl ions into the water phase and has a positive charge, which was supported by the present study.

| S-EPMC6648087 | biostudies-literature

Bioelectronic silicon nanowire devices using functional membrane proteins.

Project description:Modern means of communication rely on electric fields and currents to carry the flow of information. In contrast, biological systems follow a different paradigm that uses ion gradients and currents, flows of small molecules, and membrane electric potentials. Living organisms use a sophisticated arsenal of membrane receptors, channels, and pumps to control signal transduction to a degree that is unmatched by manmade devices. Electronic circuits that use such biological components could achieve drastically increased functionality; however, this approach requires nearly seamless integration of biological and manmade structures. We present a versatile hybrid platform for such integration that uses shielded nanowires (NWs) that are coated with a continuous lipid bilayer. We show that when shielded silicon NW transistors incorporate transmembrane peptide pores gramicidin A and alamethicin in the lipid bilayer they can achieve ionic to electronic signal transduction by using voltage-gated or chemically gated ion transport through the membrane pores.

| S-EPMC2728971 | biostudies-literature

Supramolecular Amino Acid Based Hydrogels: Probing the Contribution of Additive Molecules using NMR Spectroscopy.

Project description:Supramolecular hydrogels are composed of self-assembled solid networks that restrict the flow of water. l-Phenylalanine is the smallest molecule reported to date to form gel networks in water, and it is of particular interest due to its crystalline gel state. Single and multi-component hydrogels of l-phenylalanine are used herein as model materials to develop an NMR-based analytical approach to gain insight into the mechanisms of supramolecular gelation. Structure and composition of the gel fibres were probed using PXRD, solid-state NMR experiments and microscopic techniques. Solution-state NMR studies probed the properties of free gelator molecules in an equilibrium with bound molecules. The dynamics of exchange at the gel/solution interfaces was investigated further using high-resolution magic angle spinning (HR-MAS) and saturation transfer difference (STD) NMR experiments. This approach allowed the identification of which additive molecules contributed in modifying the material properties.

| S-EPMC5575562 | biostudies-literature

Probing Zeolite Crystal Architecture and Structural Imperfections using Differently Sized Fluorescent Organic Probe Molecules.

Project description:A micro-spectroscopic method has been developed to probe the accessibility of zeolite crystals using a series of fluorescent 4-(4-diethylaminostyryl)-1-methylpyridinium iodide (DAMPI) probes of increasing molecular size. Staining large zeolite crystals with MFI (ZSM-5) topology and subsequent mapping of the resulting fluorescence using confocal fluorescence microscopy reveal differences in structural integrity: the 90° intergrowth sections of MFI crystals are prone to develop structural imperfections, which act as entrance routes for the probes into the zeolite crystal. Polarization-dependent measurements provide evidence for the probe molecule's alignment within the MFI zeolite pore system. The developed method was extended to BEA (Beta) crystals, showing that the previously observed hourglass pattern is a general feature of BEA crystals with this morphology. Furthermore, the probes can accurately identify at which crystal faces of BEA straight or sinusoidal pores open to the surface. The results show this method can spatially resolve the architecture-dependent internal pore structure of microporous materials, which is difficult to assess using other characterization techniques such as X-ray diffraction.

| S-EPMC5434937 | biostudies-literature

Probing the Interaction of Quantum Dots with Chiral Capping Molecules Using Circular Dichroism Spectroscopy.

Project description:Circular dichroism (CD) induced at exciton transitions by chiral ligands attached to single component and core/shell colloidal quantum dots (QDs) was used to study the interactions between QDs and their capping ligands. Analysis of the CD line shapes of CdSe and CdS QDs capped with l-cysteine reveals that all of the features in the complex spectra can be assigned to the different excitonic transitions. It is shown that each transition is accompanied by a derivative line shape in the CD response, indicating that the chiral ligand can split the exciton level into two new sublevels, with opposite angular momentum, even in the absence of an external magnetic field. The role of electrons and holes in this effect could be separated by experiments on various types of core/shell QDs, and it was concluded that the induced CD is likely related to interactions of the highest occupied molecular orbitals of the ligands with the holes. Hence, CD was useful for the analysis of hole level-ligand interactions in quantum semiconductor heterostructures, with promising outlook toward better general understanding the properties of the surface of such systems.

| S-EPMC5207631 | biostudies-literature

Probing biomolecular structures and dynamics of single molecules using in-gel alternating-laser excitation.

Project description:Gel electrophoresis is a standard biochemical technique used for separating biomolecules on the basis of size and charge. Despite the use of gels in early single-molecule experiments, gel electrophoresis has not been widely adopted for single-molecule fluorescence spectroscopy. We present a novel method that combines gel electrophoresis and single-molecule fluorescence spectroscopy to simultaneously purify and analyze biomolecules in a gel matrix. Our method, in-gel alternating-laser excitation (ALEX), uses nondenaturing gels to purify biomolecular complexes of interest from free components, aggregates, and nonspecific complexes. The gel matrix also slows down translational diffusion of molecules, giving rise to long, high-resolution time traces without surface immobilization, which allow extended observations of conformational dynamics in a biologically friendly environment. We demonstrated the compatibility of this method with different types of single molecule spectroscopy techniques, including confocal detection and fluorescence-correlation spectroscopy. We demonstrated that in-gel ALEX can be used to study conformational dynamics at the millisecond time scale; by studying a DNA hairpin in gels, we directly observed fluorescence fluctuations due to conformational interconversion between folded and unfolded states. Our method is amenable to the addition of small molecules that can alter the equilibrium and dynamic properties of the system. In-gel ALEX will be a versatile tool for studying structures and dynamics of complex biomolecules and their assemblies.

| S-EPMC2799195 | biostudies-literature

Acid-Base Control of Valency within Carboranedithiol Self-Assembled Monolayers: Molecules Do the Can-Can.

Project description:We use simple acid-base chemistry to control the valency in self-assembled monolayers of two different carboranedithiol isomers on Au{111}. Monolayer formation proceeds via Au-S bonding, where manipulation of pH prior to or during deposition enables the assembly of dithiolate species, monothiol/monothiolate species, or combination. Scanning tunneling microscopy (STM) images identify two distinct binding modes in each unmodified monolayer, where simultaneous spectroscopic imaging confirms different dipole offsets for each binding mode. Density functional theory calculations and STM image simulations yield detailed understanding of molecular chemisorption modes and their relation with the STM images, including inverted contrast with respect to the geometric differences found for one isomer. Deposition conditions are modified with controlled equivalents of either acid or base, where the coordination of the molecules in the monolayers is controlled by protonating or deprotonating the second thiol/thiolate on each molecule. This control can be exercised during deposition to change the valency of the molecules in the monolayers, a process that we affectionately refer to as the "can-can." This control enables us to vary the density of molecule-substrate bonds by a factor of 2 without changing the molecular density of the monolayer.

| S-EPMC6350814 | 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