Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Revealing the catalytic kinetics and dynamics of individual Pt atoms at the single-molecule level.

ABSTRACT: SignificanceHere, with single-molecule fluorescence microscopy, we study the catalytic behavior of individual Pt atoms at single-turnover resolution, and then reveal the unique catalytic properties of Pt single-atom catalyst and the difference in catalytic properties between individual Pt atoms and Pt nanoparticles. Further density functional theory calculation indicates that unique catalytic properties of Pt single-atom catalyst could be attributed intrinsically to the unique surface properties of Pt₁-based active sites.

SUBMITTER: Liu X

PROVIDER: S-EPMC9168457 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Revealing the catalytic kinetics and dynamics of individual Pt atoms at the single-molecule level.

Liu Xiaodong X Ge Xin X Cao Jing J Xiao Yi Y Wang Yan Y Zhang Wei W Song Ping P Xu Weilin W

Proceedings of the National Academy of Sciences of the United States of America 20220329 14

SignificanceHere, with single-molecule fluorescence microscopy, we study the catalytic behavior of individual Pt atoms at single-turnover resolution, and then reveal the unique catalytic properties of Pt single-atom catalyst and the difference in catalytic properties between individual Pt atoms and Pt nanoparticles. Further density functional theory calculation indicates that unique catalytic properties of Pt single-atom catalyst could be attributed intrinsically to the unique surface properties ...[more]

PMID: 35349346

Similar Datasets

Surpassing the single-atom catalytic activity limit through paired Pt-O-Pt ensemble built from isolated Pt<sub>1</sub> atoms.

Project description:Despite the maximized metal dispersion offered by single-atom catalysts, further improvement of intrinsic activity can be hindered by the lack of neighboring metal atoms in these systems. Here we report the use of isolated Pt1 atoms on ceria as "seeds" to develop a Pt-O-Pt ensemble, which is well-represented by a Pt8O14 model cluster that retains 100% metal dispersion. The Pt atom in the ensemble is 100-1000 times more active than their single-atom Pt1/CeO2 parent in catalyzing the low-temperature CO oxidation under oxygen-rich conditions. Rather than the Pt-O-Ce interfacial catalysis, the stable catalytic unit is the Pt-O-Pt site itself without participation of oxygen from the 10-30 nm-size ceria support. Similar Pt-O-Pt sites can be built on various ceria and even alumina, distinguishable by facile activation of oxygen through the paired Pt-O-Pt atoms. Extending this design to other reaction systems is a likely outcome of the findings reported here.

| S-EPMC6707320 | biostudies-literature

Quantitative transcription factor binding kinetics at the single-molecule level.

Project description:We investigated the binding interaction between the bacteriophage lambda-repressor CI and its target DNA using total internal reflection fluorescence microscopy. Large stepwise changes in the intensity of the red fluorescent protein fused to CI were observed as it associated with and dissociated from individually labeled single-molecule DNA targets. The stochastic association and dissociation were characterized by Poisson statistics. Dark and bright intervals were measured for thousands of individual events. The exponential distribution of the intervals allowed direct determination of the association and dissociation rate constants (k(a) and k(d), respectively). We resolved in detail how k(a) and k(d) varied as a function of three control parameters: the DNA length L, the CI dimer concentration, and the binding affinity. Our results show that although interactions with nonoperator DNA sequences are observable, CI binding to the operator site is not dependent on the length of flanking nonoperator DNA.

| S-EPMC2716481 | biostudies-literature

Kinetics coming into focus: single-molecule microscopy of riboswitch dynamics.

Project description:Riboswitches are dynamic RNA motifs that are mostly embedded in the 5'-untranslated regions of bacterial mRNAs, where they regulate gene expression transcriptionally or translationally by undergoing conformational changes upon binding of a small metabolite or ion. Due to the small size of typical ligands, relatively little free energy is available from ligand binding to overcome the often high energetic barrier of reshaping RNA structure. Instead, most riboswitches appear to take advantage of the directional and hierarchical folding of RNA by employing the ligand as a structural 'linchpin' to adjust the kinetic partitioning between alternate folds. In this model, even small, local structural and kinetic effects of ligand binding can cascade into global RNA conformational changes affecting gene expression. Single-molecule (SM) microscopy tools are uniquely suited to study such kinetically controlled RNA folding since they avoid the ensemble averaging of bulk techniques that loses sight of unsynchronized, transient, and/or multi-state kinetic behavior. This review summarizes how SM methods have begun to unravel riboswitch-mediated gene regulation.

| S-EPMC6693532 | biostudies-literature

Microsecond protein dynamics observed at the single-molecule level.

Project description:How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape.

| S-EPMC4506535 | biostudies-literature

Controlling load-dependent kinetics of β-cardiac myosin at the single-molecule level.

Project description:Concepts in molecular tension sensing in biology are growing and have their origins in studies of muscle contraction. In the heart muscle, a key parameter of contractility is the detachment rate of myosin from actin, which determines the time that myosin is bound to actin in a force-producing state and, importantly, depends on the load (force) against which myosin works. Here we measure the detachment rate of single molecules of human β-cardiac myosin and its load dependence. We find that both can be modulated by both small-molecule compounds and cardiomyopathy-causing mutations. Furthermore, effects of mutations can be reversed by introducing appropriate compounds. Our results suggest that activating versus inhibitory perturbations of cardiac myosin are discriminated by the aggregate result on duty ratio, average force, and ultimately average power output and suggest that cardiac contractility can be controlled by tuning the load-dependent kinetics of single myosin molecules.

| S-EPMC6092189 | biostudies-literature

Revealing Conformational Variants of Solution-Phase Intrinsically Disordered Tau Protein at the Single-Molecule Level.

Project description:Intrinsically disordered proteins, such as tau protein, adopt a variety of conformations in solution, complicating solution-phase structural studies. We employed an anti-Brownian electrokinetic (ABEL) trap to prolong measurements of single tau proteins in solution. Once trapped, we recorded the fluorescence anisotropy to investigate the diversity of conformations sampled by the single molecules. A distribution of anisotropy values obtained from trapped tau protein is conspicuously bimodal while those obtained by trapping a globular protein or individual fluorophores are not. Time-resolved fluorescence anisotropy measurements were used to provide an explanation of the bimodal distribution as originating from a shift in the compaction of the two different families of conformations.

| S-EPMC5831721 | biostudies-literature

Conformational Dynamics of Poly(T) Single-Stranded DNA at the Single-Molecule Level.

Project description:The conformational dynamics of single-stranded DNA (ss-DNA) are implicated in the mechanisms of several key biological processes such as DNA replication and damage repair and have been modeled with those of semiflexible or flexible polymer. The high flexibility and customizability of ss-DNA also make it an excellent polymeric material for materials engineering. Polythymidine (poly(T)) is an excellent model ss-DNA as a flexible polymer since it does not form any secondary structure. However, only limited experimental results have been reported of poly(T) conformational dynamics with a very short length that is not relevant to the aforementioned processes and applications. Here, we provide the first experimental results of the conformational dynamics of poly(T) with lengths in the range of 130-170 nucleotides at the single-molecule level. Our experiments are based on single-molecule FRET and a DNA hairpin structure of which the folding kinetics are governed by the conformational dynamics of poly(T). We found that the folding kinetics deviate far from those of a flexible polymer model with a harmonic bending potential. To this end, we derived a simple model for the kinetics of DNA hairpin folding from the self-avoiding-walk (SAW). Our model describes the conformational dynamics of poly(T) very well and enables estimation of the conformational dimensionality. The estimated dimensionalities suggest that ss-DNA is completely flexible at 100 mM or a higher NaCl concentration, but not at 50 mM. These results will help understand the conformational dynamics of ss-DNA implicated in several key biological processes and maximize the utility of ss-DNA for materials engineering. Also, our system and model provide an excellent platform to investigate the conformational dynamics of ss-DNA.

| S-EPMC10034556 | biostudies-literature

Dynamics of Bacterial Signal Recognition Particle at a Single Molecule Level.

Project description:We have studied the localization and dynamics of bacterial Ffh, part of the SRP complex, its receptor FtsY, and of ribosomes in the Gamma-proteobacterium Shewanella putrefaciens. Using structured illumination microscopy, we show that ribosomes show a pronounced accumulation at the cell poles, whereas SRP and FtsY are distributed at distinct sites along the cell membrane, but they are not accumulated at the poles. Single molecule dynamics can be explained by assuming that all three proteins/complexes move as three distinguishable mobility fractions: a low mobility/static fraction may be engaged in translation, medium-fast diffusing fractions may be transition states, and high mobility populations likely represent freely diffusing molecules/complexes. Diffusion constants suggest that SRP and FtsY move together with slow-mobile ribosomes. Inhibition of transcription leads to loss of static molecules and reduction of medium-mobile fractions, in favor of freely diffusing subunits, while inhibition of translation appears to stall the medium mobile fractions. Depletion of FtsY leads to aggregation of Ffh, but not to loss of the medium mobile fraction, indicating that Ffh/SRP can bind to ribosomes independently from FtsY. Heat maps visualizing the three distinct diffusive populations show that while static molecules are mostly clustered at the cell membrane, diffusive molecules are localized throughout the cytosol. The medium fast populations show an intermediate pattern of preferential localization, suggesting that SRP/FtsY/ribosome transition states may form within the cytosol to finally find a translocon.

| S-EPMC8120034 | biostudies-literature

Cellular dynamics of the SecA ATPase at the single molecule level.

Project description:In bacteria, the SecA ATPase provides the driving force for protein secretion via the SecYEG translocon. While the dynamic interplay between SecA and SecYEG in translocation is widely appreciated, it is not clear how SecA associates with the translocon in the crowded cellular environment. We use super-resolution microscopy to directly visualize the dynamics of SecA in Escherichia coli at the single-molecule level. We find that SecA is predominantly associated with and evenly distributed along the cytoplasmic membrane as a homodimer, with only a minor cytosolic fraction. SecA moves along the cell membrane as three distinct but interconvertible diffusional populations: (1) A state loosely associated with the membrane, (2) an integral membrane form, and (3) a temporarily immobile form. Disruption of the proton-motive-force, which is essential for protein secretion, re-localizes a significant portion of SecA to the cytoplasm and results in the transient location of SecA at specific locations at the membrane. The data support a model in which SecA diffuses along the membrane surface to gain access to the SecYEG translocon.

| S-EPMC7809386 | biostudies-literature

Conformational Dynamics of DNA Polymerases Revealed at the Single-Molecule Level.

Project description:DNA polymerases are intrinsically dynamic macromolecular machines. The purpose of this review is to describe the single-molecule Förster resonance energy transfer (smFRET) methods that are used to probe the conformational dynamics of DNA polymerases, focusing on E. coli DNA polymerase I. The studies reviewed here reveal the conformational dynamics underpinning the nucleotide selection, proofreading and 5' nuclease activities of Pol I. Moreover, the mechanisms revealed for Pol I are likely employed across the DNA polymerase family. smFRET methods have also been used to examine other aspects of DNA polymerase activity.

| S-EPMC8913937 | 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