Acoustic, volumetric, compressibility and refractivity properties and reduction parameters for the ERAS and Flory models of some homologous series of amines from 298.15 to 328.15 K

The speeds of sound u, densities ? and refractive indices nD of homologous series of mono-, di-, and tri-alkylamines were measured in the temperature range from 298.15 to 328.15 K. Isentropic and isothermal compressibilities ?S and ?T, molar refraction Rm, Eykman’s constant Cm, Rao’s molar sound function R, thermal expansion coefficient a, thermal pressure coefficient ?, and reduction parameters P*, V*, and T* in frameworks of the ERAS model for associated amines and Flory model for tertiary amines have been calculated from the measured experimental data. Applicability of the Rao theory and the ERAS and Flory models have been examined and discussed for the alkyl amines.

Rapid identification of precursor cDNAs encoding five structural classes of antimicrobial peptides from pickerel frog (Rana palustris) skin secretion by single step “shotgun” cloning.

The skin secretion of the North American pickerel frog (Rana palustris) has long been known to have pronounced noxious/toxic properties and to be highly effective in defence against predators and against other sympatric amphibians. As it consists largely of a complex mixture of peptides, it has been subjected to systematic peptidomic study but there has been little focus on molecular cloning of peptide-encoding cDNAs and by deduction, the biosynthetic precursors that they encode. Here, we demonstrate that the cDNAs encoding the five major structural families of antimicrobial peptides can be elucidated by a single step “shotgun” cloning approach using a cDNA library constructed from the source material of the peptidomic studies—the defensive skin secretion itself. Using a degenerate primer pool designed to a highly conserved nucleic acid sequence 5' to the initiation codon of known antimicrobial peptide precursor transcripts, we amplified cDNA sequences representing five major classes of antimicrobial peptides, such as esculentins, brevinins, ranatuerins, palustrins and temporins. Bioinformatic comparisons of precursor open-reading frames and nucleic acid sequences revealed high degrees of structural similarities between analogous peptides of R. palustris and the Chinese bamboo odorous frog, Rana versabilis. This approach thus constitutes a robust technique that can be used either alone or ideally, in parallel with peptidomic analysis of skin secretion, to rapidly extract primary structural information on amphibian skin secretion peptides and their biosynthetic precursors.

The structural organization of aurein precursor cDNAs from the skin secretion of the Australian green and golden bell frog, Litoria aurea.

Aureins are a family of peptides (13-25 residues), some of which possess potent antimicrobial and anti-cancer properties, which have been classified into 5 subgroups based upon primary structural similarities. They were originally isolated from the defensive skin secretions of the closely related Australian bell frogs, Litoria aurea and Litoria raniformis, and of the 23 aurein peptides identified, 10 are common to both species. Using a recently developed technique, we have constructed a cDNA library from the defensive secretion of the green and golden bell frog, L. aurea, and successfully cloned a range of aurein precursor transcripts containing entire open-reading frames. All open-reading frames consisted of a putative signal peptide and an acidic pro-region followed by a single copy of aurein. The deduced precursor structures for the most active aureins (2.2 and 3.1) confirmed the presence of a C-terminal amidation motif whereas that of aurein 5.3 did not. Processed peptides corresponding in molecular mass to aureins 2.2, 2.3, 2.5, 3.1 and 5.3 were identified in the same secretion sample using LC/MS. The application of this technique thus permits parallel peptidomic and transcriptomic analyses on the same lyophilized skin secretion sample circumventing sacrifice of specimens of endangered herpetofauna.

Neuroprotective actions of a histidine analogue in models of ischemic stroke.

Histidine is a naturally occurring amino acid with antioxidant properties, which is present in low amounts in tissues throughout the body. We recently synthesized and characterized histidine analogues related to the natural dipeptide carnosine, which selectively scavenge the toxic lipid peroxidation product 4-hydroxynonenal (HNE). We now report that the histidine analogue histidyl hydrazide is effective in reducing brain damage and improving functional outcome in a mouse model of focal ischemic stroke when administered intravenously at a dose of 20 mg/kg, either 30 min before or 60 min and 3 h after the onset of middle cerebral artery occlusion. The histidine analogue also protected cultured rat primary neurons against death induced by HNE, chemical hypoxia, glucose deprivation, and combined oxygen and glucose deprivation. The histidine analogue prevented neuronal apoptosis as indicated by decreased production of cleaved caspase-3 protein. These findings suggest a therapeutic potential for HNE-scavenging histidine analogues in the treatment of stroke and related neurodegenerative conditions.

Effect of quantization of vibrations on the structural properties of crystals

We study the structural effects produced by the quantization of vibrational degrees of freedom in periodic crystals at zero temperature. To this end we introduce a methodology based on mapping a suitable subspace of the vibrational manifold and solving the Schrödinger equation in it. A number of increasingly accurate approximations ranging from the quasiharmonic approximation (QHA) to the vibrational self-consistent field (VSCF) method and the exact solution are described. A thorough analysis of the approximations is presented for model monatomic and hydrogen-bonded chains, and results are presented for a linear H-F chain where the potential-energy surface is obtained via first-principles electronic structure calculations. We focus on quantum nuclear effects on the lattice constant and show that the VSCF is an excellent approximation, meaning that correlation between modes is not extremely important. The QHA is excellent for covalently bonded mildly anharmonic systems, but it fails for hydrogen-bonded ones. In the latter, the zero-point energy exhibits a nonanalytic behavior at the lattice constant where the H atoms center, which leads to a spurious secondary minimum in the quantum-corrected energy curve. An inexpensive anharmonic approximation of noninteracting modes appears to produce rather good results for hydrogen-bonded chains for small system sizes. However, it converges to the incorrect QHA results for increasing size. Isotope effects are studied for the first-principles H-F chain. We show how the lattice constant and the H-F distance increase with decreasing mass and how the QHA proves to be insufficient to reproduce this behavior.

Structural basis of substrate selectivity in the glycerol-3-phosphate: phosphate antiporter GlpT.

Major facilitators represent the largest superfamily of secondary active transporter proteins and catalyze the transport of an enormous variety of small solute molecules across biological membranes. However, individual superfamily members, although they may be architecturally similar, exhibit strict specificity toward the substrates they transport. The structural basis of this specificity is poorly understood. A member of the major facilitator superfamily is the glycerol-3-phosphate (G3P) transporter (GlpT) from the Escherichia coli inner membrane. GlpT is an antiporter that transports G3P into the cell in exchange for inorganic phosphate (Pi). By combining large-scale molecular-dynamics simulations, mutagenesis, substrate-binding affinity, and transport activity assays on GlpT, we were able to identify key amino acid residues that confer substrate specificity upon this protein. Our studies suggest that only a few amino acid residues that line the transporter lumen act as specificity determinants. Whereas R45, K80, H165, and, to a lesser extent Y38, Y42, and Y76 contribute to recognition of both free Pi and the phosphate moiety of G3P, the residues N162, Y266, and Y393 function in recognition of only the glycerol moiety of G3P. It is the latter interactions that give the transporter a higher affinity to G3P over Pi.

Structural motifs of cholesterol nanoparticles

The growth sequence of gas-phase cholesterol clusters (Ch(N)) with up to N=36 molecules has been investigated by atomistic simulation based on an empirical force field model. The results of long annealings from high temperature show that the geometric motifs characterizing the structure of pure cholesterol crystals already appear in nanometric aggregates. In all clusters molecules tend to align along a common direction. For cluster sizes above the smallest ones, dispersion interactions among the hydrocarbon body and tails of cholesterol cooperate with hydrogen bonding to give rise to a bilayer structure. Analysis of snapshots from the annealing shows that the condensation of hydrogen bonds into a connected network of rings and chains is an important step in the self-organization of cholesterol clusters. The effect of solvation on the equilibrium properties of medium-size aggregates is investigated by short molecular dynamics simulations for the N=30 and N=40 clusters in water at near ambient conditions and in supercritical carbon dioxide at T=400 K.