Solution NMR structures of the antimicrobial peptides phylloseptin-1, -2, and -3 and biological activity: the role of charges and hydrogen bonding interactions in stabilizing helix conformations

Phylloseptins are antimicrobial peptides of 19-20 residues which are found in the skin secretions of the Phyllomedusa frogs that inhabit the tropical forests of South and Central Americas. The peptide sequences of PS-1, -2, and -3 carry an amidated C-terminus and they exhibit 74% sequence homology with major variations of only four residues close to the C-terminus. Here we investigated and compared the structures of the three phylloseptins in detail by CD- and two-dimensional NMR spectroscopies in the presence of phospholipid vesicles or in membrane-mimetic environments. Both CD and NMR spectroscopies reveal a high degree of helicity in the order PS-2> or =PS-1>PS-3, where the differences accumulate at the C-terminus. The conformational variations can be explained by taking into consideration electrostatic interactions of the negative ends of the helix dipoles with potentially cationic residues at positions 17 and 18. Whereas two are present in the sequence of PS-1 and -2 only one is present in PS-3. In conclusion, the antimicrobial phylloseptin peptides adopt alpha-helical conformations in membrane environments which are stabilized by electrostatic interactions of the helix dipole as well as other contributions such hydrophobic and capping interactions.     

Palladium(II) and platinum(II) complexes of 2-hydroxy acetophenone N(4)-ethylthiosemicarbazone - crystal structure and description of bonding properties

Reaction of H₂PtCl₄ and K₂PdCl₄ with 2-hydroxyacetophenone N(4)-ethylthiosemicarbazone, H₂Ap4Et, afforded [Pt(Ap4Et)(H₂Ap4Et)] and [Pd(Ap4Et)(H₂Ap4Et)]. Their crystal and molecular structures are reported and represent the first 1:2 thiosemicarbazone complexes with ligands having both different formal charge and denticity. The dianion, Ap4Et²⁻, coordinates in a planar conformation to palladium(II) or platinum(II) via the phenolato O, imine N and thiolato S atoms, while the neutral molecule exhibits monodentate coordination by the thione S atom. Intra-, intermolecular hydrogen bonds and C-H?π contacts lead to aggregation and a supramolecular assembly. Electronic, IR, and NMR spectral data, as well as electrochemical measurements, are included. The pK_a values of the poorly water soluble H₂Ap4Et were obtained spectrophotometrically in aqueous solutions of constant ionic strength.     

Rho-associated kinase (ROCK) inhibitor, Y27632, promotes neurite outgrowth in PC12 cells in the absence of NGF

Neurotrophins support neuronal survival and axonal regeneration after injury. To test whether local expression of Neurotrophin-3 (NT-3) would elicit axonal regeneration we lesioned the corticospinal tract (CST) at the level of the hindbrain and measured the number of axons that would grow from the unlesioned CST to the contralateral side where NT-3 was over expressed at the lumbar level of the spinal cord. An adenoviral vector that carried the rat NT-3 gene and the NGF signal peptide driven by the EF1α promoter (Adv.EF-NT-3) was used. This model enabled us to test the effects of NT-3 on axonal regeneration without confounding injury processes. Biotinylated dextran amine (BDA) was injected into the rat cortex on unlesioned side to mark CST axons 10 days postlesion. Adenoviral vectors (1 × 10⁹ pfu, Adv.EF-NT-3 or Adv.EF-LacZ) were delivered to lumbar spinal cord by retrograde transport from the sciatic nerve 4 days later. Histological examination 3 weeks later revealed that more BDA-labelled axons had grown from the unlesioned CST to the denervated side at the lumbar level. Morphometric measurements showed that a significantly larger number of BDA-labelled CST axons ( p  < 0.001) were present in the animals that were treated with Adv.EF-NT-3 than those treated with Adv.EF-LacZ. These data demonstrate that local expression of NT-3 will support axonal regeneration in the injured spinal cord without adverse effects and suggest that gene delivery of neurotrophins may be an effective strategy for nervous system repair after injury.
Acknowledgements:   Funded by NIH Grant NS35280 and by Mission Connect of the TIRR Foundation.     

Some studies on characterization of three phase partitioned chitosan

Three phase partitioning (TPP) is generally carried out by adding ammonium sulfate and t-butanol to a solution of a macromolecule. Chitosan could be obtained as an interfacial precipitate with 88% yield by subjecting 0.2% (w/v) chitosan solution to TPP with 45% (w/v) ammonium sulfate, with an equal volume of t-butanol at 40 °C. TPP resulted in structural changes which could be seen in its UV spectra, FT-IR spectra and solubility characteristics. TPP-treated chitosan also showed decreased susceptibility towards hydrolysis by chitinase. Thus, TPP can be used as a useful way of altering the properties of chitosan.     

Evolutionary Dynamics of Tat in HIV-1 Subtypes B and C

Evolutionary characteristics of HIV-1 have mostly studied focusing its structural genes, Gag, Pol and Env. However, regarding the process of HIV-1''s evolution, few studies emphasize on genetic changes in regulatory proteins. Here we investigate the evolutionary dynamics of HIV-1, targeting one of its important regulatory proteins, Tat. We performed a phylogenetic analysis and employed a Bayesian coalescent-based approach using the BEAST package to investigate the evolutionary changes in Tat over time in the process of HIV-1 evolution. HIV-1 sequences of subtypes B and C from different parts of the world were obtained from the Los Alamos database. The mean estimated nucleotide substitution rates for Tat in HIV-1 subtypes B and C were 1.53x10^-3 (95% highest probability density- HPD Interval: 1.09 x10^-3 to 2.08x10^-3) and 2.14x10^-3 (95% HPD Interval: 1.35 x10^-3 to 2.91x10^-3) per site per year, respectively, which is relatively low compared to structural proteins. The median times of the most recent common ancestors (tMRCA) were estimated to be around 1933 (95% HPD, 1907–1952) and 1956 (95% HPD, 1934–1970) for subtypes B and C, respectively. Our analysis shows that subtype C appeared in the global population two decades after the introduction of subtype B. A Gaussian Markov random field (GMRF) skyride coalescent analysis demonstrates that the early expansion rate of subtype B was quite high, rapidly progressing during the 1960s and 1970s to the early 1990s, after which the rate increased up to the 2010s. In contrast, HIV-1 subtype C exhibited a relatively slow occurrence rate until the late 1980s when there was a sharp increase up to the end of 1990s; thereafter, the rate of occurrence gradually slowed. Our study highlights the importance of examining the internal/regulatory genes of HIV-1 to understand its complete evolutionary dynamics. The study results will therefore contribute to better understanding of HIV-1 evolution.     

Characterization of yeast ribosomal DNA fragments generated by EcoR1 restriction endonuclease

Summary The action of Escherichia coli restriction endonuclease R1 (EcoR1) on DNA isolated from Saccharomyces cerevisiae (strain MAR-33) generates three predominent homogenously sized DNA fragments (species of 1.8, 2.2 and 2.5 kilo nucleotide base pairs (KB). Many DNA species of molecular weight greater than 2 million daltons can be recognized upon incomplete EcoR1 digestion of yeast DNA. Four additional DNA species ranging from 0.3–0.9 KB can be identified as the second major class of EcoR1-yeast DNA products.Hybridization with radioactive ribosomal RNA (rRNA) and competition with nonradioactive rRNA show that of the three predominent EcoR1-yeast DNA species, the 2.5 KB species hybridizes only with the 25S rRNA while the lighter 1.8 KB species hybridizes with the 18S rRNA. The intermediate DNA species of 2.2 KB hybridizes to a small extent with the 25S rRNA and could be a result of the presence of the 2.5 KB DNA species. The mass proportions and hybridization values of these 3 DNA species account for about 60% of the total ribosomal DNA (rDNA).The 5EcoR1-yeast DNA species of less than 0.9 KB (4 major and 1 minor species) hybridize to varying degrees with the 2 rRNA and can be grouped in two classes. In one class there are 3 DNA species that hybridize exclusively with the 18S rRNA. In the second class there are 2 DNA species that besides hybridizing predominently with the 25S rRNA also hybridize with the 18S rRNA. The 7 EcoR1-yeast DNA species (excluding the 2.2 KB DNA species) that hybridize with the two rRNA account for nearly a 5 million dalton DNA segment, which is very close to the anticipated gene size of rRNA precursor molecule. If the 2.2 KB DNA species is a part of the rDNA that is not transcribed or 5 sRNA then the cistron encoding the rRNA in S. cerevisiae has at least 8 EcoR1 recognition sites resulting in 8 DNA fragments upon digestion with the EcoR1. Consideration is given to the relationship of the rRNA species generated by EcoR1 digestion and the chromosomes containing ribosomal cistrons.