Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Electric Fields and Fast Protein Dynamics in Enzymes.

ABSTRACT: In recent years, there has been much discussion regarding the origin of enzymatic catalysis and whether including protein dynamics is necessary for understanding catalytic enhancement. An important contribution in this debate was made with the application of the vibrational Stark effect spectroscopy to measure electric fields in the active site. This provided a window on electric fields at the transition state in enzymatic reactions. We performed computational studies on two enzymes where we have shown that fast dynamics is part of the reaction mechanism and calculated the electric field near the bond-breaking event. We found that the fast motions that we had identified lead to an increase of the electric field, thus preparing an enzymatic configuration that is electrostatically favorable for the catalytic chemical step. We also studied the enzyme that has been the subject of Stark spectroscopy, ketosteroid isomerase, and found electric fields of a similar magnitude to the two previous examples.

SUBMITTER: Zoi I

PROVIDER: S-EPMC5769145 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Electric Fields and Fast Protein Dynamics in Enzymes.

Zoi Ioanna I Antoniou Dimitri D Schwartz Steven D SD

The journal of physical chemistry letters 20171211 24

In recent years, there has been much discussion regarding the origin of enzymatic catalysis and whether including protein dynamics is necessary for understanding catalytic enhancement. An important contribution in this debate was made with the application of the vibrational Stark effect spectroscopy to measure electric fields in the active site. This provided a window on electric fields at the transition state in enzymatic reactions. We performed computational studies on two enzymes where we hav ...[more]

PMID: 29220191

Similar Datasets

Tubulin's response to external electric fields by molecular dynamics simulations.

Project description:Tubulin heterodimers are the building blocks of microtubules and disruption of their dynamics is exploited in the treatment of cancer. Electric fields at certain frequencies and magnitudes are believed to do the same. Here, the tubulin dimer's response to external electric fields was determined by atomistic simulation. External fields from 50 to 750 kV/cm, applied for 10 ns, caused significant conformational rearrangements that were dependent upon the field's directionality. Charged and flexible regions, including the α:H1-B2 loop, β:M-loop, and C-termini, were susceptible. Closer inspection of the α:H1-B2 loop in lower strength fields revealed that these effects were consistent and proportional to field strength, and the findings indicate that external electric fields modulate the stability of microtubules through conformational changes to key loops involved in lateral contacts. We also find evidence that tubulin's curvature and elongation are affected, and external electric fields may bias tubulin towards depolymerization.

| S-EPMC6145594 | biostudies-literature

Equivalence of sessile droplet dynamics under periodic and steady electric fields.

Project description:The electrohydrodynamics of a sessile droplet under the influence of periodic and steady electric fields in microgravity conditions is theoretically investigated using an inertial lubrication model. Previous studies have revealed that a freely suspended spherical droplet with unequal conductivity and permittivity ratios exhibits distinct dynamics under periodic and equivalent steady forcing in the root mean-square sense. However, it is unclear when (if at all) such distinct dynamics occur for periodic and equivalent steady forcing in the case of sessile droplets. The equivalence between periodic and steady forcing is shown to be governed by the interfacial charge buildup, which further depends on the competition between the charge relaxation and forcing timescales. A circulation-deformation map is introduced for the sessile droplet that acts as a guideline to achieve electric field-induced wetting or dewetting as the case may be. We also demonstrate that a droplet may be rendered either more or less wetting solely by tuning the forcing frequency.

| S-EPMC8595882 | biostudies-literature

Gene expression induced by Nanosecond pulsed electric fields

Project description:We use a human whole genome microarray to analyze the effects of nanosecond pulsed electric fields on Jurkat cells with the focus on early response genes to DNA damage. Keywords: nanosecond pulsed electric fields, jurkat cells, DNA damage

2006-02-01 | GSE4106 | GEO

Protein orientation in time-dependent electric fields: orientation before destruction.

Project description:Proteins often have nonzero electric dipole moments, making them interact with external electric fields and offering a means for controlling their orientation. One application that is known to benefit from orientation control is single-particle imaging with x-ray free-electron lasers, in which diffraction is recorded from proteins in the gas phase to determine their structures. To this point, theoretical investigations into this phenomenon have assumed that the field experienced by the proteins is constant or a perfect step function, whereas any real-world pulse will be smooth. Here, we explore the possibility of orienting gas-phase proteins using time-dependent electric fields. We performed ab initio simulations to estimate the field strength required to break protein bonds, with 45 V/nm as a breaking point value. We then simulated ubiquitin in time-dependent electric fields using classical molecular dynamics. The minimal field strength required for orientation within 10 ns was on the order of 0.5 V/nm. Although high fields can be destructive for the structure, the structures in our simulations were preserved until orientation was achieved regardless of field strength, a principle we denote "orientation before destruction."

| S-EPMC8456286 | biostudies-literature

The Effects of Electric Fields on Protein Phase Behavior and Protein Crystallization Kinetics.

Project description:We experimentally studied the effects of an externally applied electric field on protein crystallization and liquid-liquid phase separation (LLPS) and its crystallization kinetics. For a surprisingly weak alternating current (AC) electric field, crystallization was found to occur in a wider region of the phase diagram, while nucleation induction times were reduced, and crystal growth rates were enhanced. LLPS on the contrary was suppressed, which diminishes the tendency for a two-step crystallization scenario. The effect of the electric field is ascribed to a change in the protein-protein interaction potential.

| S-EPMC11318033 | biostudies-literature

Electric fields drive bond homolysis.

Project description:Electric fields have been used to control and direct chemical reactions in biochemistry and enzymatic catalysis, yet directly applying external electric fields to activate reactions in bulk solution and to characterize them ex situ remains a challenge. Here we utilize the scanning tunneling microscope-based break-junction technique to investigate the electric field driven homolytic cleavage of the radical initiator 4-(methylthio)benzoic peroxyanhydride at ambient temperatures in bulk solution, without the use of co-initiators or photochemical activators. Through time-dependent ex situ quantification by high performance liquid chromatography using a UV-vis detector, we find that the electric field catalyzes the reaction. Importantly, we demonstrate that the reaction rate in a field increases linearly with the solvent dielectric constant. Using density functional theory calculations, we show that the applied electric field decreases the dissociation energy of the O-O bond and stabilizes the product relative to the reactant due to their different dipole moments.

| S-EPMC9931054 | biostudies-literature

Microsecond pulsed electric fields induce myocardial ablation by damaging mitochondria

Project description:Catheter ablation is an effective treatment to prevent recurrence of Atrial fibrillation (AF) and can be used to maintain sinus rhythm and improve symptoms of AF, but to some extent it can cause a range of adverse effects associated with catheter ablation. Pulsed electric field is a newer treatment modality to replace catheter ablation for atrial fibrillation due to its fewer side effects. Different from radiofrequency ablation, which destroys diseased myocardial tissue by thermal energy, pulsed electric field ablation achieves the purpose of atrial fibrillation ablation by inducing damage to diseased myocardial cells through irreversible electroporation. However, some experimental parameters and mechanism of pulsed electric fields remain unclear.

2023-11-30 | GSE214387 | GEO

Controlling ERK Activation Dynamics in Mammary Epithelial Cells with Alternating Electric Fields through Microelectrodes.

Project description:Amplitude, duration, and frequency of activation of the extracellular-signal-regulated kinase (ERK) pathway code distinct information to instruct cells to migrate, proliferate, or differentiate. Synchronized frequency control of ERK activation would provide a powerful approach to regulate cell behaviors. Here we demonstrated modulation of ERK activities using alternative current (AC) electric fields (EFs) applied through high-k dielectric passivated microelectrodes. Both the amplitude and frequency of ERK activation can be precisely synchronized and modulated. ERK activation in our system is independent of Faradaic currents and electroporation, thus excluding mechanisms of changes in pH, reactive oxygen species, and other electrochemical reaction. Further experiments pinpointed a mechanism of phosphorylation site of epidermal growth factor (EGF) receptor to activate the EGFR-ERK pathway, and independent of EGF. AC EFs thus provide a powerful platform for practical and precise control of EGFR-ERK pathway.

| S-EPMC6786939 | biostudies-literature

Collective migration exhibits greater sensitivity but slower dynamics of alignment to applied electric fields.

Project description:During development and disease, cells migrate collectively in response to gradients in physical, chemical and electrical cues. Despite its physiological significance and potential therapeutic applications, electrotactic collective cell movement is relatively less well understood. Here, we analyze the combined effect of intercellular interactions and electric fields on the directional migration of non-transformed mammary epithelial cells, MCF-10A. Our data show that clustered cells exhibit greater sensitivity to applied electric fields but align more slowly than isolated cells. Clustered cells achieve half-maximal directedness with an electric field that is 50% weaker than that required by isolated cells; however, clustered cells take ?2-4 fold longer to align. This trade-off in greater sensitivity and slower dynamics correlates with the slower speed and intrinsic directedness of collective movement even in the absence of an electric field. Whereas isolated cells exhibit a persistent random walk, the trajectories of clustered cells are more ballistic as evidenced by the superlinear dependence of their mean square displacement on time. Thus, intrinsically-directed, slower clustered cells take longer to redirect and align with an electric field. These findings help to define the operating space and the engineering trade-offs for using electric fields to affect cell movement in biomedical applications.

| S-EPMC4675494 | biostudies-literature

Unveiling the charge transfer dynamics steered by built-in electric fields in BiOBr photocatalysts.

Project description:Construction of internal electric fields (IEFs) is crucial to realize efficient charge separation for charge-induced redox reactions, such as water splitting and CO2 reduction. However, a quantitative understanding of the charge transfer dynamics modulated by IEFs remains elusive. Here, electron microscopy study unveils that the non-equilibrium photo-excited electrons are collectively steered by two contiguous IEFs within binary (001)/(200) facet junctions of BiOBr platelets, and they exhibit characteristic Gaussian distribution profiles on reduction facets by using metal co-catalysts as probes. An analytical model justifies the Gaussian curve and allows us to measure the diffusion length and drift distance of electrons. The charge separation efficiency, as well as photocatalytic performances, are maximized when the platelet size is about twice the drift distance, either by tailoring particle dimensions or tuning IEF-dependent drift distances. The work offers great flexibility for precisely constructing high-performance particulate photocatalysts by understanding charge transfer dynamics.

| S-EPMC9038904 | 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