Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst

Computational design of protein catalysts with enhanced stabilities for use in research and enzyme technologies is a challenging task. Using force-field calculations and phylogenetic analysis, we previously designed the haloalkane dehalogenase DhaA115 which contains 11 mutations that confer upon it outstanding thermostability (T_m = 73.5 °C; ΔT_m > 23 °C). An understanding of the structural basis of this hyperstabilization is required in order to develop computer algorithms and predictive tools. Here, we report X-ray structures of DhaA115 at 1.55 Å and 1.6 Å resolutions and their molecular dynamics trajectories, which unravel the intricate network of interactions that reinforce the αβα-sandwich architecture. Unexpectedly, mutations toward bulky aromatic amino acids at the protein surface triggered long-distance (∼27 Å) backbone changes due to cooperative effects. These cooperative interactions produced an unprecedented double-lock system that: (i) induced backbone changes, (ii) closed the molecular gates to the active site, (iii) reduced the volumes of the main and slot access tunnels, and (iv) occluded the active site. Despite these spatial restrictions, experimental tracing of the access tunnels using krypton derivative crystals demonstrates that transport of ligands is still effective. Our findings highlight key thermostabilization effects and provide a structural basis for designing new thermostable protein catalysts.

Illustration of cooperative thermostabilization effects of the double-lock system that: (i) induced backbone changes, (ii) closed the molecular gates, (iii) reduced the volumes of the main and slot access tunnels, and (iv) occluded the active site.     

4‐Acetamido‐3,3,5,5‐[2H4]‐2,2,6,6‐tetra­([2H3]methyl)piperidin‐1‐yloxyl 0.33‐hydrate

The asymmetric unit of the title compound, C₁₁H₅D₁₆N₂O₂·0.33H₂O, is formed by three crystallographically independent piperidin‐1‐yloxyl mol­ecules and a mol­ecule of water. The mol­ecules are crosslinked by nine hydrogen bonds into layers parallel with the ac plane. The water mol­ecule contributes to the stability of the low‐symmetry arrangement by four hydrogen bonds.     

Multi-element characterization of silicon nitride powders by atomic and mass spectrometric solution methods

A sample pretreatment technique for silicon nitride involving digestion and matrix/traces separation was developed by means of radiotracers and applied to analysis of this material by inductively coupled plasma atomic emission spectrometry, inductively coupled plasma mass spectrometry and graphite furnace atomic absorption spectrometry. The results obtained for a high purity silicon nitride material by these methods are compared each with the other and with those obtained by neutron activation analysis. The limits of detection and the capabilities of the methods are compared and discussed.     

An automated method for the analysis of stable isotope labeling data in proteomics

An algorithm is presented for the generation of a reliable peptide component peak table from liquid chromatography-mass spectrometry (LC-MS) and subsequent quantitative analysis of stable isotope coded peptide samples. The method uses chemical noise filtering, charge state fitting, and deisotoping toward improved analysis of complex peptide samples. Overlapping peptide signals in mass spectra were deconvoluted by correlation with modeled peptide isotopic peak profiles. Isotopic peak profiles for peptides were generated in silico from a protein database producing reference model distributions. Doublets of heavy and light labeled peak clusters were identified and compared to provide differential quantification of pairs of stable isotope coded peptides. Algorithms were evaluated using peptides from digests of a single protein and a seven-protein mixture that had been differentially coded with stable isotope labeling agents and mixed in known ratios. The experimental results correlated well with known mixing ratios.     

Generalized reinhardt domains

In this paper we investigate a class of Lie group actions on , the so-calledpolar actions, that naturally generalize the standard actions. For a domain invariant under such an action (i.e., a generalized Reinhardt domain) we characterize the invariant plurisubharmonic functions and determine the envelope of holomorphy in geometric terms. For a generalized Reinhardt domain containing the origin of we also compute its automorphism group. Supported in part by NSF Grant 8602020     

The atomic-level structure of bandgap engineered double perovskite alloys Cs2AgIn1−xFexCl6

Although lead-free halide double perovskites are considered as promising alternatives to lead halide perovskites for optoelectronic applications, state-of-the-art double perovskites are limited by their large bandgap. The doping/alloying strategy, key to bandgap engineering in traditional semiconductors, has also been employed to tune the bandgap of halide double perovskites. However, this strategy has yet to generate new double perovskites with suitable bandgaps for practical applications, partially due to the lack of fundamental understanding of how the doping/alloying affects the atomic-level structure. Here, we take the benchmark double perovskite Cs₂AgInCl₆ as an example to reveal the atomic-level structure of double perovskite alloys (DPAs) Cs₂AgIn_1−xFe_xCl₆ (x = 0–1) by employing solid-state nuclear magnetic resonance (ssNMR). The presence of paramagnetic alloying ions (e.g. Fe³⁺ in this case) in double perovskites makes it possible to investigate the nuclear relaxation times, providing a straightforward approach to understand the distribution of paramagnetic alloying ions. Our results indicate that paramagnetic Fe³⁺ replaces diamagnetic In³⁺ in the Cs₂AgInCl₆ lattice with the formation of [FeCl₆]³⁻·[AgCl₆]⁵⁻ domains, which show different sizes and distribution modes in different alloying ratios. This work provides new insights into the atomic-level structure of bandgap engineered DPAs, which is of critical significance in developing efficient optoelectronic/spintronic devices.

Through Fe³⁺-alloying, the bandgap of benchmark double perovskite Cs₂AgInCl₆ can be tuned from 2.8 eV to 1.6 eV. The atomic-level structure of Cs₂AgIn_1−xFe_xCl₆ was revealed by solid-state nuclear magnetic resonance (ssNMR).     

Heteroaromatic thioether-boronic acid cross-coupling under neutral reaction conditions

[reaction: see text] Pi-deficient heteroaromatic thioethers undergo efficient palladium-catalyzed cross-coupling with boronic acids mediated by copper(I) thiophene-2-carboxylate.     

Dicyanamide complexes of copper(II), nickel(II) and cobalt(II) with benzimidazole and its 2-alkyl-derivatives

Summary Dicyanamide complexes of Cu^II, Ni^II and Co^II of the type M[N(CN)₂]₂L₂, where L = benzimidazole, 2-methyl- or 2-ethylbenzimidazole, have been prepared and studied by spectroscopy and magnetochemistry. The complexes, except for Co[N(CN)₂]₂ (benzimidazole)₂, are six-coordinate, involving bidentate bridging dicyanamide groups. While the Ni^II complexes have practically octahedral structures, the Cu^II complexes are pseudooctahedral with similar tetragonal distortion. The ligand field strength in these complexes depends mainly on the steric effect of the benzimidazole ligands. The Co^II complex of benzimidazole is monomeric tetrahedral, but that of 2-ethylbenzimidazole is tetragonal octahedral. The oridging function of dicyanamide in the six-coordinate complexes is realized either through both cyanide or through amide and cyanide nitrogens. The complex Cu[N(CN)₂]₂ (2-methylbenzimidazole)₂ is a weak antiferromagnet (J = -0.1 cm^–1), exhibiting under ca. 15 K a long-range antiferromagnetic ordering.