High Accuracy Protein Structures from Minimal Sparse Paramagnetic Solid‐State NMR Restraints

There is a pressing need for new computational tools to integrate data from diverse experimental approaches in structural biology. We present a strategy that combines sparse paramagnetic solid‐state NMR restraints with physics‐based atomistic simulations. Our approach explicitly accounts for uncertainty in the interpretation of experimental data through the use of a semi‐quantitative mapping between the data and the restraint energy that is calibrated by extensive simulations. We apply our approach to solid‐state NMR data for the model protein GB1 labeled with Cu²⁺‐EDTA at six different sites. We are able to determine the structure to 0.9 Å accuracy within a single day of computation on a GPU cluster. We further show that in some cases, the data from only a single paramagnetic tag are sufficient for accurate folding.     

Tyrosine nitration of human ERK1 introduces an intra-hydrogen bond by molecular dynamics simulations

Structural Chemistry - ERK1 is an important kinase in Ras–Raf–MEK signaling. We have recently demonstrated by mass spectrometry that Tyr210 of ERK1 can be nitrated, and the nitration...     

Investigation of Ti/CuO interface by X-ray photoelectron spectroscopy and atomic force microscopy

The Ti/CuO interface has been studied by the techniques of X-ray photoelectron spectroscopy and atomic force microscopy. Thin films of titanium were deposited on a CuO substrate at room temperature by the e-beam technique. The photoelectron spectra of titanium and copper were found to exhibit significant chemical interaction at the interface. The titanium overlayer was observed to get oxidized to TiO₂, while the CuO was observed to get reduced to elemental copper. This chemical interaction was observed to occur until a thickness of 7 nm of the titanium overlayer. For thicknesses greater than this value, the presence of unreacted titanium in the sample was detected. Barrier characteristics at the Ti/CuO interface were also carried out for substrate temperatures of 300°C, 400°C, 500°C, and 600°C as a function of the titanium overlayer thickness. A linear trend in the barrier thickness of the overlayer was observed between 400°C and 600°C substrate temperatures. The atomic force microscopy micrographs of the unannealed samples depicted layer-by-layer growth of elemental titanium on copper. At the Ti/CuO interface in such samples, the micrographs exhibited island formation of TiO₂ corresponding to the Volmer-Weber growth model. This formation has been interpreted as the relaxation in the strain energy. The percentage coverage of the underlying substrate by the TiO₂ islands showed a linear trend for the thicknesses of the titanium overlayer investigated. The average size of these islands also showed a linear trend as a function of the thickness of the overlayer.     

Desingularization of a Steady Vortex Pair in the Lake Equation

Potential Analysis - We construct a family of steady solutions of the lake model perturbed by some small Coriolis force, that converge to a singular vortex pair. The desingularized solutions are...     

Scalable Biosynthesis of the Seaweed Neurochemical,Kainic Acid

Kainic acid, the flagship member of the kainoid family of natural neurochemicals, is a widely used neuropharmacological agent that helped unravel the key role of ionotropic glutamate receptors, including the kainate receptor, in the central nervous system. Worldwide shortages of this seaweed natural product in the year 2000 prompted numerous chemical syntheses, including scalable preparations with as few as six‐steps. Herein we report the discovery and characterization of the concise two‐enzyme biosynthetic pathway to kainic acid from l ‐glutamic acid and dimethylallyl pyrophosphate in red macroalgae and show that the biosynthetic genes are co‐clustered in genomes of Digenea simplex and Palmaria palmata. Moreover, we applied a key biosynthetic α‐ketoglutarate‐dependent dioxygenase enzyme in a biotransformation methodology to efficiently construct kainic acid on the gram scale. This study establishes both the feasibility of mining seaweed genomes for their biotechnological prowess.     

Acid/Base‐Triggered Switching of Circularly Polarized Luminescence and Electronic Circular Dichroism in Organic and Organometallic Helicenes

Electronic circular dichroism and circularly polarized luminescence acid/base switching activity has been demonstrated in helicene‐bipyridine proligand 1 a and in its “rollover” cycloplatinated derivative 2 a . Whereas proligand 1 a displays a strong bathochromic shift (>160 nm) of the nonpolarized and circularly polarized luminescence upon protonation, complex 2 a displays slightly stronger emission. This strikingly different behavior between singlet emission in the organic helicene and triplet emission in the organometallic derivative has been rationalized by using quantum‐chemical calculations. The very large bathochromic shift of the emission observed upon protonation of azahelicene‐bipyridine 1 a has been attributed to the decrease in aromaticity (promoting a charge‐transfer‐type transition rather than a π–π* transition) as well as an increase in the HOMO–LUMO character of the transition and stabilization of the LUMO level upon protonation.