Correction: Electrochemically shape-controlled synthesis of great stellated dodecahedral Au nanocrystals with high-index facets for nitrogen reduction to ammonia.

Correction for 'Electrochemically shape-controlled synthesis of great stellated dodecahedral Au nanocrystals with high-index facets for nitrogen reduction to ammonia' by Yu-Chen Jiang et al., Chem. Commun.

Affinity of Skp to OmpC revealed by single-molecule detection.

Outer membrane proteins (OMPs) are essential to gram-negative bacteria, and molecular chaperones prevent the OMPs from aggregation in the periplasm during the OMPs biogenesis. Skp is one of the molecular chaperones for this purpose. Here, we combined single-molecule fluorescence resonance energy transfer and fluorescence correlation spectroscopy to study the affinity and stoichiometric ratio of Skp in its binding with OmpC at the single-molecule level.

Electrochemically shape-controlled synthesis of great stellated dodecahedral Au nanocrystals with high-index facets for nitrogen reduction to ammonia.

Au great stellated dodecahedra (GSD), one of the Kepler-Poinsot solids, are synthesized by an electrochemical double-step potential method in a choline chloride-urea based deep eutectic solvent. The as-synthesized Au GSD are bound by high-index {331} facets and exhibit excellent electrocatalytic performance for the nitrogen reduction reaction with a high NH3 yield rate (49.96 μg h-1 cm-2) and faradaic efficiency (28.

Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models.

DNA glycosylase is responsible for repairing DNA damage to maintain the genome stability and integrity. However, how glycosylase can efficiently and accurately recognize DNA lesions across the enormous DNA genome remains elusive. It has been hypothesized that glycosylase translocates along the DNA by alternating between a fast but low-accuracy diffusion mode and a slow but high-accuracy mode when searching for DNA lesions.

Molecular mechanism of networking among DegP, Skp and SurA in periplasm for biogenesis of outer membrane proteins.

The biogenesis of outer membrane proteins (OMPs) is an extremely challenging process. In the periplasm of Escherichia coli, a group of quality control factors work together to exercise the safe-guard and quality control of OMPs. DegP, Skp and SurA are the three most prominent ones.

Excavated cubic platinum-iridium alloy nanocrystals with high-index facets as highly efficient electrocatalysts in N fixation to NH.

Excavated cubic PtIr alloy nanocrystals enclosed by high-index {710} facets exhibit excellent electrocatalytic properties for the nitrogen reduction reaction (NRR) with a high faradaic efficiency (40.8%) and NH production rate (28 μg h cm). The presence of Ir on the Pt stepped surface suppresses the hydrogen evolution reaction (HER) and accelerates the NRR.

Single-molecule study on conformational dynamics of M.HhaI.

We found that apo DNA methyltransferase M.HhaI under the physiological salt concentration does not possess the structure characterized by X-ray crystallography; instead, it interchanges between prefolded and unfolded states. Only after binding to the substrate, it transforms into a crystal-structure-like state.

Single-Molecule Detection Reveals Different Roles of Skp and SurA as Chaperones.

Skp and SurA are both periplasmic chaperones involved in the biogenesis of Escherichia coli β-barrel outer membrane proteins (OMPs). It is commonly assumed that SurA plays a major role whereas Skp is a minor factor. However, there is no molecular evidence for whether their roles are redundant.

Determination of Equilibrium Constant and Relative Brightness in FRET-FCS by Including the Third-Order Correlations.

Fluorescence correlation spectroscopy (FCS) encodes the information on the equilibrium constant (K), the relative fluorescence brightness of fluorophore (Q), and the forward and backward reaction rate constants (k and k) on a physical or chemical relaxation. However, it has been a long-standing problem to completely resolve the FCS data to get the thermodynamic and kinetic information. Recently, we have solved the problem for fluorescence autocorrelation spectroscopy (FACS).

Urea hydrogen bond donor-mediated synthesis of high-index faceted platinum concave nanocubes grown on multi-walled carbon nanotubes and their enhanced electrocatalytic activity.

We have reported, for the first time, in situ growth of high-index {hk0} faceted concave Pt nanocubes on multi-walled carbon nanotubes (CNTs) via an electrochemical method in choline chloride-urea (ChCl-U) based deep eutectic solvents (DESs). Mechanistic studies indicate that a urea hydrogen bond donor (HBD) plays a key role in the formation of concave Pt nanocubes, in which the urea HBD preferentially adsorbs onto the {100} faces and blocks the growth of nanocrystals along the 〈100〉 axis. The as-prepared concave Pt nanocubes are characterized to be enclosed mainly with high-index {710}, {610} and {510} facets.

Kinetic insights into the temperature dependence of DNA strand cleavage and religation by topoisomerase III from the hyperthermophile Sulfolobus solfataricus.

All cellular organisms encode type IA topoisomerases which catalyze DNA topological changes essential for DNA transactions. However, the kinetics of the reaction catalyzed by these enzymes remains poorly characterized. Here we measured the rapid kinetics of template binding, cleavage and religation by Sso topo III, a type IA topoisomerase from the hyperthermophilic archaeon Sulfolobus solfataricus, by using a novel FRET/PIFE-based method in a stopped-flow spectrometer.

Seeds and Potentials Mediated Synthesis of High-Index Faceted Gold Nanocrystals with Enhanced Electrocatalytic Activities.

Because high-index facets (HIFs) possess high surface energy, the metal nanoparticles enclosed with HIFs are eliminated during their growth in a conventional shape-controlled synthesis due to the thermodynamics that drives the particles minimizing their total surface energy. This study develops a double-step potential method to prepare an unprecedentedly stellated Au nanocrystals (NCs) bounded by high-index {711} and {331} facets in deep eutectic solvent (DES) medium. The formation of Au NCs bounded by HIFs was systematically studied.

Determination of Equilibrium Constant and Relative Brightness in Fluorescence Correlation Spectroscopy by Considering Third-Order Correlations.

Fluorescence correlation spectroscopy (FCS) is a powerful tool to investigate molecular diffusion and relaxations, which may be utilized to study many problems such as molecular size and aggregation, chemical reaction, molecular transportation and motion, and various kinds of physical and chemical relaxations. This article focuses on a problem related to using the relaxation term to study a reaction. If two species with different fluorescence photon emission efficiencies are connected by a reaction, the kinetic and equilibrium properties will be manifested in the relaxation term of the FCS curve.

Scanning Single-Molecule Fluorescence Correlation Spectroscopy Enables Kinetics Study of DNA Hairpin Folding with a Time Window from Microseconds to Seconds.

Single-molecule fluorescence measurements have been widely used to explore kinetics and dynamics of biological systems. Among them, single-molecule imaging (SMI) is good at tracking processes slower than tens of milliseconds, whereas fluorescence correlation spectroscopy (FCS) is good at probing processes faster than submilliseconds. However, there is still shortage of simple yet effective single-molecule fluorescence method to cover the time-scale between submilliseconds and tens of milliseconds.

Accurate placement of substrate RNA by Gar1 in H/ACA RNA-guided pseudouridylation.

H/ACA RNA-guided ribonucleoprotein particle (RNP), the most complicated RNA pseudouridylase so far known, uses H/ACA guide RNA for substrate capture and four proteins (Cbf5, Nop10, L7Ae and Gar1) for pseudouridylation. Although it was shown that Gar1 not only facilitates the product release, but also enhances the catalytic activity, the chemical role that Gar1 plays in this complicated machinery is largely unknown. Kinetics measurement on Pyrococcus furiosus RNPs at different temperatures making use of fluorescence anisotropy showed that Gar1 reduces the catalytic barrier through affecting the activation entropy instead of enthalpy.

Periplasmic quality control in biogenesis of outer membrane proteins.

The β-barrel outer membrane proteins (OMPs) are integral membrane proteins that reside in the outer membrane of Gram-negative bacteria and perform a diverse range of biological functions. Synthesized in the cytoplasm, OMPs must be transported across the inner membrane and through the periplasmic space before they are assembled in the outer membrane. In Escherichia coli, Skp, SurA and DegP are the most prominent factors identified to guide OMPs across the periplasm and to play the role of quality control.

EF-G catalyzes tRNA translocation by disrupting interactions between decoding center and codon-anticodon duplex.

During translation, elongation factor G (EF-G) catalyzes the translocation of tRNA2-mRNA inside the ribosome. Translocation is coupled to a cycle of conformational rearrangements of the ribosomal machinery, and how EF-G initiates translocation remains unresolved. Here we performed systematic mutagenesis of Escherichia coli EF-G and analyzed inhibitory single-site mutants of EF-G that preserved pretranslocation (Pre)-state ribosomes with tRNAs in A/P and P/E sites (Pre-EF-G).

Dynamics of spontaneous flipping of a mismatched base in DNA duplex.

DNA base flipping is a fundamental theme in DNA biophysics. The dynamics for a B-DNA base to spontaneously flip out of the double helix has significant implications in various DNA-protein interactions but are still poorly understood. The spontaneous base-flipping rate obtained previously via the imino proton exchange assay is most likely the rate of base wobbling instead of flipping.

Identification of FkpA as a key quality control factor for the biogenesis of outer membrane proteins under heat shock conditions.

The outer membrane proteins (OMPs) of Gram-negative bacterial cells, as well as the mitochondrion and chloroplast organelles, possess unique and highly stable β-barrel structures. Biogenesis of OMPs in Escherichia coli involves such periplasmic chaperones as SurA and Skp. In this study, we found that the ΔsurA Δskp double-deletion strain of E.

Single-molecule detection reveals knot sliding in TrmD denaturation.

An increasing number of proteins are found to contain a knot in their polypeptide chain. Although some studies have looked into the folding mechanism of knotted proteins, why and how these complex topologies form are still far from being fully answered. Moreover, no experimental information about how the knot moves during the protein-folding process is available.

Amplitude of Relaxations in Fluorescence Correlation Spectroscopy for Fluorophores That Diffuse Together.

The amplitude of chemical relaxations in fluorescence correlation spectroscopy (FCS) is an important parameter that directly relates to not only the equilibrium constant of the relaxations but also the number of individual fluorophores that diffuse together. In this Letter we answer the question how exactly the amplitude of the relaxations in FCS changes with respect to the number of identical fluorophores on one cargo. We anchored tetramethylrhodamine molecules onto each arm of a DNA Holliday junction molecule so that the codiffusing dyes were capable of performing independent fluorescent fluctuations.

Direct observation of the uptake of outer membrane proteins by the periplasmic chaperone Skp.

The transportation of membrane proteins through the aqueous subcellular space is an important and challenging process. Its molecular mechanism and the associated structural change are poorly understood. Periplasmic chaperones, such as Skp in Escherichia coli, play key roles in the transportation and protection of outer membrane proteins (OMPs) in Gram-negative bacteria.

Kinetic and thermodynamic characterization of the reaction pathway of box H/ACA RNA-guided pseudouridine formation.

The box H/ACA RNA-guided pseudouridine synthase is a complicated ribonucleoprotein enzyme that recruits substrate via both the guide RNA and the catalytic subunit Cbf5. Structural studies have revealed multiple conformations of the enzyme, but a quantitative description of the reaction pathway is still lacking. Using fluorescence correlation spectroscopy, we here measured the equilibrium dissociation constants and kinetic association and dissociation rates of substrate and product complexes mimicking various reaction intermediate states.

Panorama of DNA hairpin folding observed via diffusion-decelerated fluorescence correlation spectroscopy.

Based on a confocal microscopy platform, we extended the FCS time window by three orders of magnitude to the s timescale by attaching a polystyrene microsphere. We simultaneously monitored the relaxations of multiple intermediates involved in DNA hairpin folding, thus offering a much more detailed view of the kinetics of hairpin folding experimentally.