Tackling Sample‐Related Artifacts in Membrane FCS Using Parallel SAF and UAF Detection

The complex shape and plasticity of cells is an intricate issue for the measurement of molecular diffusion in plasma membranes by fluorescence correlation spectroscopy (FCS). An important precondition for accurate diffusion measurements is a sufficient flatness of the membrane over the considered region and the absence of non‐membrane‐bound fluorescence diffusion. A method is presented to identify axial motion components caused by a non‐ideal geometry of the membrane based on simultaneous measurement of the fluorescence emitted above and below the critical angle of the specimen/glass interface. Thereby, two detection volumes are generated that are laterally coincident, but differ in their axial penetration of the specimen. The similarity between the intensity tracks of the supercritical angle fluorescence (SAF) and the undercritical angle fluorescence (UAF) strongly depends on the membrane flatness and intracellular fluorescence, and can help to avoid sample‐related artifacts in the diffusion measurement.     

Multivalent Gold Glycoclusters: High Affinity Molecular Recognition by Bacterial Lectin PA‐IL

Multivalent protein‐carbohydrate interactions are involved in the initial stages of many fundamental biological and pathological processes through lectin–carbohydrate binding. The design of high affinity ligands is therefore necessary to study, inhibit and control the processes governed through carbohydrate recognition by their lectin receptors. Carbohydrate‐functionalised gold nanoclusters (glyconanoparticles, GNPs) show promising potential as multivalent tools for studies in fundamental glycobiology research as well as biomedical applications. Here we present the synthesis and characterisation of galactose functionalised GNPs and their effectiveness as binding partners for PA‐IL lectin from Pseudomonas aeruginosa. Interactions were evaluated by hemagglutination inhibition (HIA), surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) assays. Results show that the gold nanoparticle platform displays a significant cluster glycoside effect for presenting carbohydrate ligands with almost a 3000‐fold increase in binding compared with a monovalent reference probe in free solution. The most effective GNP exhibited a dissociation constant (K_d) of 50 nM per monosaccharide, the most effective ligand of PA‐IL measured to date; another demonstration of the potential of glyco‐nanotechnology towards multivalent tools and potent anti‐adhesives for the prevention of pathogen invasion. The influence of ligand presentation density on their recognition by protein receptors is also demonstrated.     

Characterization of the 1st and 2nd EF-hands of NADPH oxidase 5 by fluorescence, isothermal titration calorimetry, and circular dichroism

Background

Superoxide generated by non-phagocytic NADPH oxidases (NOXs) is of growing importance for physiology and pathobiology. The calcium binding domain (CaBD) of NOX5 contains four EF-hands, each binding one calcium ion. To better understand the metal binding properties of the 1^st and 2^nd EF-hands, we characterized the N-terminal half of CaBD (NCaBD) and its calcium-binding knockout mutants.

Results

The isothermal titration calorimetry measurement for NCaBD reveals that the calcium binding of two EF-hands are loosely associated with each other and can be treated as independent binding events. However, the Ca²⁺ binding studies on NCaBD(E31Q) and NCaBD(E63Q) showed their binding constants to be 6.5 × 10⁵ and 5.0 × 10² M^-1 with ??Hs of -14 and -4 kJ/mol, respectively, suggesting that intrinsic calcium binding for the 1^st non-canonical EF-hand is largely enhanced by the binding of Ca²⁺ to the 2^nd canonical EF-hand. The fluorescence quenching and CD spectra support a conformational change upon Ca²⁺ binding, which changes Trp residues toward a more non-polar and exposed environment and also increases its ??-helix secondary structure content. All measurements exclude Mg²⁺-binding in NCaBD.

Conclusions

We demonstrated that the 1^st non-canonical EF-hand of NOX5 has very weak Ca²⁺ binding affinity compared with the 2^nd canonical EF-hand. Both EF-hands interact with each other in a cooperative manner to enhance their Ca²⁺ binding affinity. Our characterization reveals that the two EF-hands in the N-terminal NOX5 are Ca²⁺ specific.

Graphical abstract

     

Metal organic frameworks as nitric oxide catalysts

The use of metal organic frameworks (MOFs) for the catalytic production of nitric oxide (NO) is reported. In this account we demonstrate the use of Cu(3)(BTC)(2) as a catalyst for the generation of NO from the biologically occurring substrate, S-nitrosocysteine (CysNO). The MOF catalyst was evaluated as an NO generator by monitoring the evolution of NO in real time via chemiluminescence. The addition of 2, 10, and 15-fold excess CysNO to MOF-Cu(II) sites and cysteine (CysH) resulted in catalytic turnover of the active sites and nearly 100% theoretical yield of the NO product. Control experiments without the MOF present did not yield appreciable NO generation. In separate studies the MOF was found to be reusable over successive iterations of CysNO additions without loss of activity. Subsequently, the MOF catalyst was confirmed to remain structurally intact by pXRD and ATR-IR following reaction with CysNO and CysH.     

Connectivity and binding‐site recognition: Applications relevant to drug design

Here, we describe a family of methods based on residue–residue connectivity for characterizing binding sites and apply variants of the method to various types of protein–ligand complexes including proteases, allosteric‐binding sites, correctly and incorrectly docked poses, and inhibitors of protein–protein interactions. Residues within ligand‐binding sites have about 25% more contact neighbors than surface residues in general; high‐connectivity residues are found in contact with the ligand in 84% of all complexes studied. In addition, a k‐means algorithm was developed that may be useful for identifying potential binding sites with no obvious geometric or connectivity features. The analysis was primarily carried out on 61 protein–ligand structures from the MEROPS protease database, 250 protein–ligand structures from the PDBSelect (25%), and 30 protein–protein complexes. Analysis of four proteases with crystal structures for multiple bound ligands has shown that residues with high connectivity tend to have less variable side‐chain conformation. The relevance to drug design is discussed in terms of identifying allosteric‐binding sites, distinguishing between alternative docked poses and designing protein interface inhibitors. Taken together, this data indicate that residue–residue connectivity is highly relevant to medicinal chemistry. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Integrability and conservation laws for two systems of hydrodynamic type derived from the Toda and Volterra systems

We prove that two particular systems of hydrodynamic type can be represented as systems of conservation laws, and that they decouple into non-interacting integrable subsystems. The systems of hydrodynamic type in question were previously constructed, via a matrix partial differential equation, from the Lax pairs for the classical Toda and Volterra systems. The decoupling is guaranteed by the vanishing of the Nijenhuis tensor for each system; integrability of the non-interacting subsystems, thus each system as a whole, is proven for low eigenvalue multiplicities.     

Gusts within plant canopies are extreme value processes

Plant canopy turbulence is characterised by energetic high-velocity downdrafts (sweeps) and updrafts (ejections) that punctuate otherwise quiescent flow and thereby make the dominant contribution to turbulent transport. It is suggested that this turbulence provides a natural setting for the emergence of extreme value processes. The suggestion is supported by simulation data obtained from Lagrangian probability density function models. Predicted wind speed frequency distributions within the lower portions of plant canopies are consistent with observations and are very well represented by Gumbel (extreme value) distributions. This is interpreted as a signature of strong (maximal) intermittent gusts making the dominant contribution to the turbulence. The findings complement the apparent ubiquity of generalised Gumbel distributions of global quantities in boundary-layer turbulence, equilibrium phase transitions and non-equilibrium models with self-organised criticality. In these examples, however, there are no known direct relationships between the global quantities and extreme value processes. The new findings are interesting from a practical perspective because correct parametrisation of the wind speed frequency distribution is required for the accurate quantification of seed abscission and the removal of pollens and passively released pathogenic spores from plant surfaces.