Evolution of Thyroglobulin Loop Kinetics in EpCAM

Epithelial cell-activating molecule (EpCAM) is an important cancer biomarker and therapeutic target given its elevated expression in epithelial cancers. EpCAM is a type I transmembrane protein that forms cis-dimers along the thyroglobulin type-1A-like domain (TYD) in the extracellular region. The thyroglobulin loop (TY loop) within the TYD is structurally dynamic in the monomer state of human EpCAM, binding reversibly to a TYD site. However, it is not known if this flexibility is prevalent across different species. Here, we conduct over 17 μs of all-atom molecular dynamics simulations to study EpCAM TY loop kinetics of five different species, including human, mouse, chicken, frog, and fish. We find that the TY loop remains dynamic across evolution. In addition to the TYD binding site, we discover a second binding site for the TY loop in the C-terminal domain (CTD). Calculations of the dissociation rate constants from the simulation trajectories suggest a differential binding pattern of fish EpCAM and other organisms. Whereas fish TY loop has comparable binding for both TYD and CTD sites, the TY loops of other species preferably bind the TYD site. A hybrid construct of fish EpCAM with human TY loop restores the TYD binding preference, suggesting robust effects of the TY loop sequence on its dynamic behavior. Our findings provide insights into the structural dynamics of EpCAM and its implication in physiological functions.

Surface plasmon resonance unveils important pitfalls of enzyme-linked immunoassay for the detection of anti-infliximab antibodies in patients’ sera

Measurements of serum concentrations of therapeutic antibodies and anti-drug antibodies (ADA) can support clinical decisions for the management of non-responders, optimizing the therapy. In the present study we compared the results obtained by classical ELISA and a recently proposed surface plasmon resonance (SPR)-based immunoassay, in 76 patients receiving infliximab for inflammatory bowel diseases. The two methods indicated very similar serum concentrations of the drug, but there were striking differences as regards ADA. All the sera showing ADA by ELISA (14) also showed ADA by SPR, but the absolute amounts were different, being 7–490 times higher with SPR, with no correlation. Eight patients showed ADA only with SPR, and these ADA had significantly faster dissociation rate constants than those detectable by both SPR and ELISA. The underestimation, or the lack of detection, of ADA by ELISA is likely to reflect the long incubation steps which favor dissociation of the patient’s low-affinity ADA, while the commercial, high-affinity anti-infliximab antibodies used for the calibration curve do not dissociate. This problem is less important with SPR, which monitors binding in real time. The possibility offered by SPR to detect ADA in patients otherwise considered ADA-negative by ELISA could have important implications for clinicians.

Mechanism of a Disassembly Driven Sensing System Studied by Stopped-Flow Kinetics

<div> Mechanistic studies were carried out on the kinetics for the assembly of a DimerDye (DD12) and the binding of the monomeric DimerDye (DD1) with nicotine in aqueous buffer and artificial saliva. DD12 is non-fluorescent, while monomeric DD1 and DD1-nicotine fluoresce. Binding isotherms were determined from steady-state fluorescence experiments. The report includes measurements of the steady-state fluorescence at pHs 2.2, 6.3 and 12.1, and stopped-flow kinetic data for the homodimerization forming DD12 and DD1-nicotine formation in buffer and artificial saliva. Analysis of the homodimerization kinetics led to the recovery of the association and dissociation rate constants for DD12. These rate constants were used in the global analysis for the coupled kinetics for DD1-nicotine formation, which led to the determination of the association and dissociation rate constants for nicotine binding to DD1.</div>

Mechanism of a Disassembly Driven Sensing System Studied by Stopped-Flow Kinetics

<div> Mechanistic studies were carried out on the kinetics for the assembly of a DimerDye (DD12) and the binding of the monomeric DimerDye (DD1) with nicotine in aqueous buffer and artificial saliva. DD12 is non-fluorescent, while monomeric DD1 and DD1-nicotine fluoresce. Binding isotherms were determined from steady-state fluorescence experiments. The report includes measurements of the steady-state fluorescence at pHs 2.2, 6.3 and 12.1, and stopped-flow kinetic data for the homodimerization forming DD12 and DD1-nicotine formation in buffer and artificial saliva. Analysis of the homodimerization kinetics led to the recovery of the association and dissociation rate constants for DD12. These rate constants were used in the global analysis for the coupled kinetics for DD1-nicotine formation, which led to the determination of the association and dissociation rate constants for nicotine binding to DD1.</div>

Mycobacterial and Human Ferrous Nitrobindins: Spectroscopic and Reactivity Properties

Structural and functional properties of ferrous Mycobacterium tuberculosis (Mt-Nb) and human (Hs-Nb) nitrobindins (Nbs) were investigated. At pH 7.0 and 25.0 °C, the unliganded Fe(II) species is penta-coordinated and unlike most other hemoproteins no pH-dependence of its coordination was detected over the pH range between 2.2 and 7.0. Further, despite a very open distal side of the heme pocket (as also indicated by the vanishingly small geminate recombination of CO for both Nbs), which exposes the heme pocket to the bulk solvent, their reactivity toward ligands, such as CO and NO, is significantly slower than in most hemoproteins, envisaging either a proximal barrier for ligand binding and/or crowding of H2O molecules in the distal side of the heme pocket which impairs ligand binding to the heme Fe-atom. On the other hand, liganded species display already at pH 7.0 and 25 °C a severe weakening (in the case of CO) and a cleavage (in the case of NO) of the proximal Fe-His bond, suggesting that the ligand-linked movement of the Fe(II) atom onto the heme plane brings about a marked lengthening of the proximal Fe-imidazole bond, eventually leading to its rupture. This structural evidence is accompanied by a marked enhancement of both ligands dissociation rate constants. As a whole, these data clearly indicate that structural–functional relationships in Nbs strongly differ from what observed in mammalian and truncated hemoproteins, suggesting that Nbs play a functional role clearly distinct from other eukaryotic and prokaryotic hemoproteins.

Genotype-phenotype map of an RNA-ligand complex

RNA-ligand interactions play important roles in biology and biotechnology, but they often involve complex three-dimensional folding of RNA and are difficult to predict. To systematically explore the phenotypic landscape of an RNA-ligand complex, we used microarrays to investigate all possible single and double mutants of the 49-nt RNA aptamer Broccoli bound to the fluorophore DFHBI-1T. We collected more than seven million fluorescence measurements in varying conditions, and inferred dissociation rate constants, spectral shifts, and intragenic epistasis. Our results reveal an unexpectedly complex phenotypic landscape, in which mutations near the fluorophore binding pocket modulated magnesium-, potassium- and fluorophore-binding and fluorescence spectra, while distal mutations influenced structural stability and fluorescence intensity. We trained a machine learning model that accurately predicted RNA secondary structure from local epistatic interactions, despite the presence of G-quadruplexes and other noncanonical structures. Our experimental platform will facilitate the discovery and analysis of new RNA-ligand interactions.

Cadherin clusters stabilized by a combination of specific and nonspecific cis-interactions

We demonstrate a combined experimental and computational approach for the quantitative characterization of lateral interactions between membrane-associated proteins. In particular, weak, lateral (cis) interactions between E-cadherin extracellular domains tethered to supported lipid bilayers, were studied using a combination of dynamic single-molecule Förster Resonance Energy Transfer (FRET) and kinetic Monte Carlo (kMC) simulations. Cadherins are intercellular adhesion proteins that assemble into clusters at cell-cell contacts through cis- and trans- (adhesive) interactions. A detailed and quantitative understanding of cis-clustering has been hindered by a lack of experimental approaches capable of detecting and quantifying lateral interactions between proteins on membranes. Here single-molecule intermolecular FRET measurements of wild-type E-cadherin and cis-interaction mutants combined with simulations demonstrate that both nonspecific and specific cis-interactions contribute to lateral clustering on lipid bilayers. Moreover, the intermolecular binding and dissociation rate constants are quantitatively and independently determined, demonstrating an approach that is generalizable for other interacting proteins.

Cadherin Clusters Stabilized by a Combination of Specific and Nonspecific Cis-Interactions

We demonstrate a combined experimental and computational approach for the quantitative characterization of lateral interactions between membrane-associated proteins. In particular, weak, lateral (cis) interactions between E-cadherin extracellular domains tethered to supported lipid bilayers, were studied using a combination of dynamic single-molecule Förster Resonance Energy Transfer (FRET) and kinetic Monte Carlo (kMC) simulations. Cadherins are intercellular adhesion proteins that assemble into clusters at cell-cell contacts through cis- and trans- (adhesive) interactions. A detailed and quantitative understanding of cis-clustering has been hindered by a lack of experimental approaches capable of detecting and quantifying lateral interactions between proteins on membranes. Here single-molecule intermolecular FRET measurements of wild-type E-cadherin and cis-interaction mutants combined with simulations demonstrate that both nonspecific and specific cis-interactions contribute to lateral clustering on lipid bilayers. Moreover, the intermolecular binding and dissociation rate constants are quantitatively and independently determined, demonstrating an approach that is generalizable for other interacting proteins.

A DFT Insight into the Tuning Effect of Potassium Promoter on the Formation of Carbon Atoms via Carburization Gases Dissociation on Iron-Based Catalysts

The research of the formation mechanism of iron carbides is significant to design the high-performance catalysts for the Fischer–Tropsch synthesis (FTS) process. In this paper, the effect of potassium promoter on the formation of atomic carbon via carburization gases dissociation on the iron-based catalyst, the C2H4, C2H2 and CO/H2 adsorption energies and dissociation paths as well as the rate constants of the corresponding elementary steps are investigated by DFT on the Fe(110), Fe(110)-K2O, Fe(211) and Fe(211)-K2O surfaces. The calculation results demonstrated that the K2O promoter can modify the capabilities of surface C formation via the thermodynamic method as well as the kinetical method. The K2O promoter can increase the CO adsorption energy while decreasing the C2H4 adsorption energy both on Fe(110) and Fe(211) surfaces. Kinetically, via tuning the catalyst surfaces from Fe(110) to Fe(211), the K2O promoter can inhibit the ability of C2H4/C2H2 dissociation to atomic carbon, while enhancing the ability of CO/H2 decomposition to atomic carbon. The C2H4/C2H2 dissociation rate constants on Fe(211) and Fe(211)-K2O are about 107 times slower than that on Fe(110) and Fe(110)-K2O, whereas the dissociation rate constants of CO/H2 on Fe(211) are about 106 times faster than that on Fe(110), and about 107 times faster on Fe(211)-K2O than on Fe(110)-K2O.