Insight into the folding inhibition of the HIV-1 protease by a small peptide

It has recently been shown that the highly protected segments 24-34 (S2) and 83-93 (S8) of each of the two 99-mers of human immunodeficiency virus type 1 protease play an essential role in the folding of the monomers, giving rise to the so-called (postcritical) folding nucleus ((FN) minimum condensation unit ensuring folding) when they dock. This scenario received further support from model calculations that demonstrated that the peptide p-S8, displaying an amino acid sequence identical to the corresponding (83-93) segment of the monomer, can be used to interfere with the formation of the FN and eventually to inhibit folding by docking the fragment 24-34. Experiments in vitro and in cells infected with ex vivo wild-type and multiresistant HIV isolates confirm that the inhibition power of p-S8 is robust. On the other hand, there is no direct evidence demonstrating the validity of the proposed mechanism of inhibition associated with p-S8. To shed light on this question and to provide the basis for the design of a molecule mimetic to p-S8, to be used as lead of an eventual drug against AIDS, we study, in this paper, with the help of all-atom simulations in explicit solvent and the novel method of metadynamics combined with parallel tempering: a), the free energy and the equilibrium structure of each of the peptides p-S2 and p-S8; b), the details of the docking mechanism of the two peptides and the free energy associated with this process. Whereas p-S8 is found to be well structured, p-S2 is rather flexible, wrapping itself around p-S8 to give rise to the FN, which is stabilized by three particular hydrogen bonds.     

A practical selective synthesis of mixed short/long chains glycerophosphocholines

Glycerophosphorylcholine (GPC) is transformed into the cyclic stannylene derivatives, which are selectively acylated to 1-acyl-2-lyso-glycerophosphocholines. The reaction is effective using C-2 to C-16 acid chlorides in 2-propanol. After solvent replacement the lyso-phospholipid (lyso-PL) is subjected to a second acylation using acid anhydrides in methylene chloride. A series of 1(2)-short-2(1)-long-diacyl-glycerophosphocholines are obtained in high yields and selectivity. No diacylation product was detected. In order to detect mixed-chain lipids with inverted disposition of acyl chains, the long chain was introduced first and the thus resulting isomeric compounds compared by NMR. An NMR method was developed in order to determine the positional purity of the isomeric compounds.     

Ghrelin has novel vascular actions that mimic PI 3-kinase-dependent actions of insulin to stimulate production of NO from endothelial cells

Ghrelin is an orexigenic peptide hormone secreted by the stomach. In patients with metabolic syndrome and low ghrelin levels, intra-arterial ghrelin administration acutely improves their endothelial dysfunction. Therefore, we hypothesized that ghrelin activates endothelial nitric oxide synthase (eNOS) in vascular endothelium, resulting in increased production of nitric oxide (NO) using signaling pathways shared in common with the insulin receptor. Similar to insulin, ghrelin acutely stimulated increased production of NO in bovine aortic endothelial cells (BAEC) in primary culture (assessed using NO-specific fluorescent dye 4,5-diaminofluorescein) in a time- and dose-dependent manner. Production of NO in response to ghrelin (100 nM, 10 min) in human aortic endothelial cells was blocked by pretreatment of cells with NG-nitro-L-arginine methyl ester (nitric oxide synthase inhibitor), wortmannin [phosphatidylinositol (PI) 3-kinase inhibitor], or (D-Lys3)-GHRP-6 (selective antagonist of ghrelin receptor GHSR-1a), as well as by knockdown of GHSR-1a using small-interfering (si) RNA (but not by mitogen/extracellular signal-regulated kinase inhibitor PD-98059). Moreover, ghrelin stimulated increased phosphorylation of Akt (Ser473) and eNOS (Akt phosphorylation site Ser1179) that was inhibitable by knockdown of GHSR-1a using siRNA or by pretreatment of cells with wortmannin but not with PD-98059. Ghrelin also stimulated phosphorylation of mitogen-activated protein (MAP) kinase in BAEC. However, unlike insulin, ghrelin did not stimulate MAP kinase-dependent secretion of the vasoconstrictor endothelin-1 from BAEC. We conclude that ghrelin has novel vascular actions to acutely stimulate production of NO in endothelium using a signaling pathway that involves GHSR-1a, PI 3-kinase, Akt, and eNOS. Our findings may be relevant to developing novel therapeutic strategies to treat diabetes and related diseases characterized by reciprocal relationships between endothelial dysfunction and insulin resistance.     

The Paleocene–Eocene Thermal Maximum as recorded by Tethyan planktonic foraminifera in the Forada section (northern Italy)

The Forada section in the Venetian Pre-Alps of northern Italy represents an expanded record of the Paleocene–Eocene Thermal Maximum (PETM) at a depositional paleodepth of about 1 km ± 0.5 km. High-resolution planktonic foraminiferal analysis of this section, in a time interval of approximately 1.3 Myr across the Paleocene/Eocene boundary, reveals striking faunal changes that allow the identification of eight phases (a–h). The late Paleocene was represented by stable, warm and oligotrophic surface water conditions (phase a). Unstable environmental conditions start well before the onset of PETM (ca. 150 kyr, phase b) and involved a change towards eutrophy, as marked by the increase of Subbotina and the concomitant decrease of Morozovella. This step is also characterized by enhanced fragmentation and dissolution.The interval corresponding to the main body of the carbon isotope excursion (CIE) is characterized by a marked increase of Acarinina, though with some differences in the species composition and relative abundance, both in high-and low-latitudes, particularly in the Tethyan area. Forada is no exception to this pattern. However, at Forada, two prominent peaks in abundance of acarininids are recorded ca. 30 kyr prior to the onset of the CIE, thus suggesting an increase in temperature heralding the onset of the PETM (phase c). Interestingly, the lower peak in abundance of Acarinina just precedes the 1‰ carbon isotope negative shift occurring below the onset of the main CIE. The basalmost Eocene, corresponding to the lower part of CIE curve, is represented by intense planktonic foraminiferal dissolution, implying an extraordinary rise of the CCD. This interval has an estimated duration of about 16 kyr (phase d).The dominance of acarininids in the lower part of the CIE (phase e, f; ca. 14 and 22.5 kyr) is interpreted as a consequence of the extreme warmth coupled with eutrophic conditions characterizing the Forada depositional environment at that time. These acarininids include at Forada also the temporally constrained Acarinina sibaiyaensis and A. africana. The morphological similarity between these peculiar species with the radially elongated chambered forms characterizing the Cretaceous anoxic events, suggests the hypothesis that depletion of oxygen in the upper water column might have been one of the factors causing their conspicuous occurrence at the PETM.The recovery in abundance of the specialized morozovellids and of other planktonic foraminiferal groups (e.g., biserials, globanomalinids, igorinids, planorotalids and pseudohastigerinids), occurring in the middle part of the CIE (ca. 30 kyr after the onset of the PETM), indicates an initial environmental recovery (phase g). A new stable state is definitely reached in the upper part of the Forada section where the relative proportions of the main component of planktonic foraminiferal assemblages move towards values similar to those of the late Paleocene conditions (phase h). However, the perturbation during the PETM produced significant changes in the ocean geochemistry that endured after the PETM event, as testified by the prominent high carbonate dissolution characterizing the marly levels, and the large variability in relative abundance among different components of the planktonic foraminiferal assemblages. These striking oscillations were not present in the latest Paleocene.     

A unified physiological framework of transitions between seizures,sustained ictal activity and depolarization block at the single neuron level

Journal of Computational Neuroscience - The majority of seizures recorded in humans and experimental animal models can be described by a generic phenomenological mathematical model, the Epileptor....     

Network-Specific Synchronization of Electrical Slow-Wave Oscillations Regulates Sleep Drive in Drosophila

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