Browse
Submit Data
Databases
API
Help

Dataset Information

49 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A protocol to measure slow protein dynamics of the cholera toxin B pentamers using broadband dielectric spectroscopy.

ABSTRACT: The present protocol describes how to measure experimentally the slow protein dynamics that take place upon the thermal unfolding of the B subunit cholera toxin pentamers using broadband dielectric spectroscopy (BDS) in weakly hydrated and nanoconfined conditions. Transient unfolding intermediates, rarely identified otherwise, are revealed thanks to the B subunit's remarkable heat resistance up to 180°C and distinct molecular dynamics. The frequencies detected experimentally are consistent with the spatiotemporal scales of motions of molecular dynamics simulation. For complete details on the use and execution of this protocol, please refer to Bourgeat et al. (2021, 2019).

SUBMITTER: Bourgeat L

PROVIDER: S-EPMC9304676 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A protocol to measure slow protein dynamics of the cholera toxin B pentamers using broadband dielectric spectroscopy.

Bourgeat Laetitia L Pacini Lorenza L Serghei Anatoli A Lesieur Claire C

STAR protocols 20220718 3

The present protocol describes how to measure experimentally the slow protein dynamics that take place upon the thermal unfolding of the B subunit cholera toxin pentamers using broadband dielectric spectroscopy (BDS) in weakly hydrated and nanoconfined conditions. Transient unfolding intermediates, rarely identified otherwise, are revealed thanks to the B subunit's remarkable heat resistance up to 180°C and distinct molecular dynamics. The frequencies detected experimentally are consistent with ...[more]

PMID: 35874473

Similar Datasets

Experimental Protein Molecular Dynamics: Broadband Dielectric Spectroscopy coupled with nanoconfinement.

Project description:Protein dynamics covers multiple spatiotemporal scale processes, among which slow motions, not much understood even though they are underlying protein folding and protein functions. Protein slow motions are associated with structural heterogeneity, short-lived and poorly populated conformations, hard to detect individually. In addition, they involve collective motions of many atoms, not easily tracked by simulation and experimental devices. Here we propose a biophysical approach, coupling geometrical nanoconfinement and broadband dielectric spectroscopy (BDS), which distinguishes protein conformations by their respective molecular dynamics. In particular, protein-unfolding intermediates, usually poorly populated in macroscopic solutions are detected. The protein dynamics is observed under unusual conditions (sample nanoconfinement and dehydration) highlighting the robustness of protein structure and protein dynamics to a variety of conditions consistent with protein sustainability. The protein dielectric signals evolve with the temperature of thermal treatments indicating sensitivity to atomic and molecular interaction changes triggered by the protein thermal unfolding. As dipole fluctuations depend on both collective large-scale motions and local motions, the approach offers a prospect to track in-depth unfolding events.

| S-EPMC6884508 | biostudies-literature

Broadband Dielectric Spectroscopy Study of Biobased Poly(alkylene 2,5-furanoate)s' Molecular Dynamics.

Project description:Poly(2,5-alkylene furanoate)s are bio-based, smart, and innovative polymers that are considered the most promising materials to replace oil-based plastics. These polymers can be synthesized using ecofriendly approaches, starting from renewable sources, and result into final products with properties comparable and even better than those presented by their terephthalic counterparts. In this work, we present the molecular dynamics of four 100% bio-based poly(alkylene 2,5-furanoate)s, using broadband dielectric spectroscopy measurements that covered a wide temperature and frequency range. We unveiled complex local relaxations, characterized by the simultaneous presence of two components, which were dependent on thermal treatment. The segmental relaxation showed relaxation times and strengths depending on the glycolic subunit length, which were furthermore confirmed by high-frequency experiments in the molten region of the polymers. Our results allowed determining structure-property relations that are able to provide further understanding about the excellent barrier properties of poly(alkylene 2,5-furanoate)s. In addition, we provide results of high industrial interest during polymer processing for possible industrial applications of poly(alkylene furanoate)s.

| S-EPMC7361705 | biostudies-literature

Cholera toxin B subunits assemble into pentamers--proposition of a fly-casting mechanism.

Project description:The cholera toxin B pentamer (CtxB(5)), which belongs to the AB(5) toxin family, is used as a model study for protein assembly. The effect of the pH on the reassembly of the toxin was investigated using immunochemical, electrophoretic and spectroscopic methods. Three pH-dependent steps were identified during the toxin reassembly: (i) acquisition of a fully assembly-competent fold by the CtxB monomer, (ii) association of CtxB monomer into oligomers, (iii) acquisition of the native fold by the CtxB pentamer. The results show that CtxB(5) and the related heat labile enterotoxin LTB(5) have distinct mechanisms of assembly despite sharing high sequence identity (84%) and almost identical atomic structures. The difference can be pinpointed to four histidines which are spread along the protein sequence and may act together. Thus, most of the toxin B amino acids appear negligible for the assembly, raising the possibility that assembly is driven by a small network of amino acids instead of involving all of them.

| S-EPMC3006222 | biostudies-literature

Slow water dynamics in dehydrated human Jurkat T cells evaluated by dielectric spectroscopy with the Bruggeman-Hanai equation.

Project description:The picosecond orientational dynamics of intracellular water was measured by dielectric spectroscopy, with the aim of revealing the effects of cryoprotective agents (CPAs) on biological cells. As a first step, Jurkat cells (human T lymphocyte cells) suspended in aqueous sucrose solutions of different concentrations ranging from 0.3 M (isotonic) to 0.9 M (hypertonic) were examined at 25 °C with a frequency range up to 43.5 GHz. The Bruggeman-Hanai equation was employed to obtain a cellular dielectric spectrum without extracellular contributions from the measured complex permittivity of the cell suspensions. By analyzing the γ process around 1010 Hz based on the Debye relaxation function, two types of water (bulk-like water and hydration water with slower molecular dynamics) were observed. An increase in the fraction of intracellular slower water was observed in the dehydrated cells which had a highly concentrated environment of biomolecules.

| S-EPMC10334875 | biostudies-literature

Nanoscale dipole dynamics of protein membranes studied by broadband dielectric microscopy.

Project description:We investigate the nearfield dipole mobility of protein membranes in a wide frequency range from 3 kHz to 10 GHz. The results of our nanoscale dielectric images and spectra of bacteriorhodopsin (bR) reveal Debye relaxations with time constants of τ ∼ 2 ns and τ ∼ 100 ns being characteristic of the dipole moments of the bR retinal and α-helices, respectively. However, the dipole mobility and therefore the protein biophysical function depend critically on the amount of surface water surrounding the protein, and the characteristic mobility in the secondary structure is only observed for humidity levels <30%. Our results have been achieved by adding the frequency as a second fundamental dimension to quantitative dielectric microscopy. The key elements for the success of this advanced technique are the employed heterodyne detection scheme, the broadband electrical signal source, a high frequency optimized cabling, development of calibration procedures and precise finite element modelling. Our study demonstrates the exciting possibilities of broadband dielectric microscopy for the investigation of dynamic processes in cell bioelectricity at the individual molecular level. Furthermore, the technique may shed light on local dynamic processes in related materials science applications like semiconductor research or nano-electronics.

| S-EPMC6457197 | biostudies-literature

Broadband achromatic dielectric metalenses.

Project description:Metasurfaces offer a unique platform to precisely control optical wavefronts and enable the realization of flat lenses, or metalenses, which have the potential to substantially reduce the size and complexity of imaging systems and to realize new imaging modalities. However, it is a major challenge to create achromatic metalenses that produce a single focal length over a broad wavelength range because of the difficulty in simultaneously engineering phase profiles at distinct wavelengths on a single metasurface. For practical applications, there is a further challenge to create broadband achromatic metalenses that work in the transmission mode for incident light waves with any arbitrary polarization state. We developed a design methodology and created libraries of meta-units-building blocks of metasurfaces-with complex cross-sectional geometries to provide diverse phase dispersions (phase as a function of wavelength), which is crucial for creating broadband achromatic metalenses. We elucidated the fundamental limitations of achromatic metalens performance by deriving mathematical equations that govern the tradeoffs between phase dispersion and achievable lens parameters, including the lens diameter, numerical aperture (NA), and bandwidth of achromatic operation. We experimentally demonstrated several dielectric achromatic metalenses reaching the fundamental limitations. These metalenses work in the transmission mode with polarization-independent focusing efficiencies up to 50% and continuously provide a near-constant focal length over λ = 1200-1650 nm. These unprecedented properties represent a major advance compared to the state of the art and a major step toward practical implementations of metalenses.

| S-EPMC6220161 | biostudies-literature

Redox chemistry in the pigment eumelanin as a function of temperature using broadband dielectric spectroscopy.

Project description:Conductive biomolecular systems are investigated for their promise of new technologies. One biomolecular material that has garnered interest for device applications is eumelanin. Its unusual properties have led to its incorporation in a wide set of platforms including transistor devices and batteries. Much of eumelanin's conductive properties are due to a solid state redox comproportionation reaction. However, most of the work that has been done to demonstrate the role of the redox chemistry in eumelanin has been via control of eumelanin's hydration content with scant attention given to temperature dependent behavior. Here we demonstrate for the first time consistency between hydration and temperature effects for the comproportionation conductivity model utilizing dielectric spectroscopy, heat capacity measurements, frequency scaling phenomena and recognizing that activation energies in the range of ∼0.5 eV correspond to proton dissociation events. Our results demonstrate that biomolecular conductivity models should account for temperature and hydration effects coherently.

| S-EPMC9060503 | biostudies-literature

Interfacial polarization of in vivo rat sciatic nerve with crush injury studied via broadband dielectric spectroscopy.

Project description:Electrical stimulation is one of the candidates for elongation-driven regeneration of damaged peripheral nerves. Different organs and tissues have an inherent cell structure and size. This leads to variation in the tissue-specific electrical properties of the frequency of interfacial polarization. Although nervous tissues have a membrane potential, the electrical reaction inside these tissues following electrical stimulation from outside remains unexplored. Furthermore, the pathophysiological reaction of an injured nerve is unclear. Here, we investigated the electrical reaction of injured and non-injured rat sciatic nerves via broadband dielectric spectroscopy. Crush injured and non-injured sciatic nerves of six 12-week-old male Lewis rats were used, 6 days after infliction of the injury. Both sides of the nerves (with and without injury) were exposed, and impedance measurements were performed at room temperature (approximately 25°C) at frequencies ranging from 100 mHz to 5.5 MHz and electric potential ranging from 0.100 to 1.00 V. The measured interfacial polarization potentially originated from the polarization by ion transport around nerve membranes at frequencies between 3.2 kHz and 1.6 MHz. The polarization strength of the injured nerves was smaller than that of non-injured nerves. However, the difference in polarization between injured and non-injured nerves might be caused by inflammation and edema. The suitable frequency range of the interfacial polarization can be expected to be critical for electrical stimulation of injured peripheral nerves.

| S-EPMC8171940 | biostudies-literature

Inverse-Designed Broadband All-Dielectric Electromagnetic Metadevices.

Project description:This paper presents a platform combining an inverse electromagnetic design computational method with additive manufacturing to design and fabricate all-dielectric metadevices. As opposed to conventional flat metasurface-based devices that are composed of resonant building blocks resulting in narrow band operation, the proposed design approach creates non-resonant, broadband (Δλ/λ up to >50%) metadevices based on low-index dielectric materials. High-efficiency (transmission >60%), thin (≤2λ) metadevices capable of polarization splitting, beam bending, and focusing are proposed. Experimental demonstrations are performed at millimeter-wave frequencies using 3D-printed devices. The proposed platform can be readily applied to the design and fabrication of electromagnetic and photonic metadevices spanning microwave to optical frequencies.

| S-EPMC5778146 | biostudies-literature

Broadband angular spectrum differentiation using dielectric metasurfaces.

Project description:Signal processing is of critical importance for various science and technology fields. Analog optical processing can provide an effective solution to perform large-scale and real-time data processing, superior to its digital counterparts, which have the disadvantages of low operation speed and large energy consumption. As an important branch of modern optics, Fourier optics exhibits great potential for analog optical image processing, for instance for edge detection. While these operations have been commonly explored to manipulate the spatial content of an image, mathematical operations that act directly over the angular spectrum of an image have not been pursued. Here, we demonstrate manipulation of the angular spectrum of an image, and in particular its differentiation, using dielectric metasurfaces operating across the whole visible spectrum. We experimentally show that this technique can be used to enhance desired portions of the angular spectrum of an image. Our approach can be extended to develop more general angular spectrum analog meta-processors, and may open opportunities for optical analog data processing and biological imaging.

| S-EPMC10933489 | 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