Syntheses, structures and bioactivities of cadmium(II) complexes with a tridentate heterocyclic N- and S-ligand

Four cadmium(II) complexes of the semirigid tridentate ligand 8-[(pyridin-4-yl)methylthio] quinoline (TQMP4, L), namely, [CdL₂](ClO₄)₂ (1), [Cd(L)Br₂] (2), [Cd₂(L)₂(NO₃)₄] (3), and [Cd₂(L)₂I₄] (4), have been prepared by the methods of layering and the diffusing of diethyl ether. The structures of the complexes have been identified by elemental analysis (EA), infrared spectra (IR) and single-crystal diffraction. The different coordination modes of the ligands and counter anions result in a 2D (4, 4) net structure in complex 1, a 1D polymer chain in complex 2, and 0D binuclear rings in complexes 3 and 4. Their antibacterial and antifungal activities were also tested.     

Molecular phylogeny of Ceropegia (Asclepiadoideae, Apocynaceae) from Indian Western Ghats

Ceropegia includes more than 200 species distributed in the Old World ranging from the Canary Islands to Australia. In India, there are about 50 species described on a morphological basis as belonging to Ceropegia, and most of them are endemic to the Western Ghats. To investigate evolutionary relationships among Indian Ceropegia taxa and their allies, a phylogenetic analysis was conducted to include 31 Indian taxa of Ceropegia and Brachystelma and their congeners from other geographical regions using nuclear ribosomal internal transcribed spacer (ITS) and three noncoding chloroplast DNA (cpDNA) sequences, including intergenic spacers trnT-L and trnL-F, and trnL intron. The Western Ghats Ceropegia species were found to be most closely related to Indian Brachystelma, with the two genera being placed sister to each other in the ITS phylogeny or with the Brachystelma clade nested within one of the two subclades of Indian Ceropegia in the cpDNA phylogeny. In contrast, Ceropegia species from other regions and African Brachystelma all formed separate clades basal to the Indian Ceropegia–Brachystelma clade. Thus, it can be concluded that the classical morphology-based delineation of the two genera needs revision to reflect their phylogenetic relationships, which are more in accordance with their geographical origin than with morphology.     

Tuning the conformational properties of the prion peptide

Previously, we disclosed that O‐linked glycosylation of Ser‐132 or Ser‐135 could dramatically change the amyloidogenic property of the hamster prion peptide (sequence 108–144). This peptide, which corresponds to the flexible loop and the first β‐strand in the structure of the prion protein, is a random coil when it is initially dissolved in buffer, but amyloid fibrils are formed with time. Thus, it offers a convenient model system to observe and compare how different chemical modifications and sequence mutations alter the amyloidogenic property of the peptide within a reasonable experimental time frame. In our earlier study, aside from uncovering a site‐specificity of the glycosylation on the fibrillogenesis, different effects of α‐GalNAc and β‐GlcNAc were observed. In this work, we explore further how different sugar configurations affect the conformational property of the polypeptide chain. We compare the effects of O‐linked glycosylation by the common sugars α‐GalNAc, β‐GlcNAc with their non‐native analogs β‐GalNAc, α‐GlcNAc in an effort to uncover the origin of the sugar‐specificity on the fibril formation. We find that the anomeric configuration of the sugar is the most important factor affecting the fibrillogenesis. Sugars with the glycosidic bond in the α‐configuration at Ser‐135 have a dramatic inhibitory effect on the structural conversion of the glycosylated peptide. Because O‐glycosylation of Ser‐135 with α‐linked sugars also promote the formation of three slowly converting conformations at the site of glycosylation, we surmise that the amyloidogenic property of the peptide is related to its conformational flexibility, and the proclivity of this region of the peptide to undergo the structural conversion from the random coil to form the β‐structure. Upon O‐glycosylation with an α‐linked sugar, this conversion is inhibited and the nucleation of fibril formation is largely retarded. Consistent with this scenario, Arg‐136 is the residue most affected in the TOCSY NMR spectra of the glycosylated peptides, other than the serine site modified. In addition, when Arg‐136 is substituted by Gly, a mutation that should provide higher structural flexibility in this part of the peptide, the amyloidogenic property of the peptide is greatly enhanced, and the inhibition effect of glycosylation is largely diminished. These results are consistent with Ser‐135 and Arg‐136 being part of the kink region involved in the structural conversion. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry

Disordered or unstructured regions of proteins, while often very important biologically, can pose significant challenges for resonance assignment and three‐dimensional structure determination of the ordered regions of proteins by NMR methods. In this article, we demonstrate the application of ¹H/²H exchange mass spectrometry (DXMS) for the rapid identification of disordered segments of proteins and design of protein constructs that are more suitable for structural analysis by NMR. In this benchmark study, DXMS is applied to five NMR protein targets chosen from the Northeast Structural Genomics project. These data were then used to design optimized constructs for three partially disordered proteins. Truncated proteins obtained by deletion of disordered N‐ and C‐terminal tails were evaluated using ¹H‐¹⁵N HSQC and ¹H‐¹⁵N heteronuclear NOE NMR experiments to assess their structural integrity. These constructs provide significantly improved NMR spectra, with minimal structural perturbations to the ordered regions of the protein structure. As a representative example, we compare the solution structures of the full length and DXMS‐based truncated construct for a 77‐residue partially disordered DUF896 family protein YnzC from Bacillus subtilis, where deletion of the disordered residues (ca. 40% of the protein) does not affect the native structure. In addition, we demonstrate that throughput of the DXMS process can be increased by analyzing mixtures of up to four proteins without reducing the sequence coverage for each protein. Our results demonstrate that DXMS can serve as a central component of a process for optimizing protein constructs for NMR structure determination. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Asymmetric Friedel‐Crafts alkylations of indoles with dialkyl 3‐oxoprop‐1‐enylphosphonates: Organocatalytic enantioselective synthesis of α‐indolyl phosphonates

Organocatalytic enantioselective synthesis of α‐indolyl phosphonates has been successfully carried out via asymmetric Friedel‐Crafts alkylation of substituted indoles with (E)‐dialkyl 3‐oxoprop‐1‐enylphosphonates in 48–82% yield and 73–96% ee. Chirality, 2009. © 2008 Wiley‐Liss, Inc.     

Effects of amantadine on the dynamics of membrane-bound influenza A M2 transmembrane peptide studied by NMR relaxation

The molecular motions of membrane proteins in liquid-crystalline lipid bilayers lie at the interface between motions in isotropic liquids and in solids. Specifically, membrane proteins can undergo whole-body uniaxial diffusion on the microsecond time scale. In this work, we investigate the ¹H rotating-frame spin-lattice relaxation (T _1ρ) caused by the uniaxial diffusion of the influenza A M2 transmembrane peptide (M2TMP), which forms a tetrameric proton channel in lipid bilayers. This uniaxial diffusion was proved before by ²H, ¹⁵N and ¹³C NMR lineshapes of M2TMP in DLPC bilayers. When bound to an inhibitor, amantadine, the protein exhibits significantly narrower linewidths at physiological temperature. We now investigate the origin of this line narrowing through temperature-dependent ¹H T _1ρ relaxation times in the absence and presence of amantadine. Analysis of the temperature dependence indicates that amantadine decreases the correlation time of motion from 2.8 ± 0.9 μs for the apo peptide to 0.89 ± 0.41 μs for the bound peptide at 313 K. Thus the line narrowing of the bound peptide is due to better avoidance of the NMR time scale and suppression of intermediate time scale broadening. The faster diffusion of the bound peptide is due to the higher attempt rate of motion, suggesting that amantadine creates better-packed and more cohesive helical bundles. Analysis of the temperature dependence of $ { \ln }\left( {T_{1\rho }^{ - 1} } \right) $ indicates that the activation energy of motion increased from 14.0 ± 4.0 kJ/mol for the apo peptide to 23.3 ± 6.2 kJ/mol for the bound peptide. This higher activation energy indicates that excess amantadine outside the protein channel in the lipid bilayer increases the membrane viscosity. Thus, the protein-bound amantadine speeds up the diffusion of the helical bundles while the excess amantadine in the bilayer increases the membrane viscosity.