An Allosteric Mechanism for Inhibiting HIV-1 Integrase with a Small Molecule

HIV-1 integrase (IN) is a validated target for developing antiretroviral inhibitors. Using affinity acetylation and mass spectrometric (MS) analysis, we previously identified a tetra-acetylated inhibitor (2E)-3-[3,4-bis(acetoxy)phenyl]-2-propenoate-N-[(2E)-3-[3,4-bis(acetyloxy)phenyl]-1-oxo-2-propenyl]-L-serine methyl ester; compound 1] that selectively modified Lys173 at the IN dimer interface. Here we extend our efforts to dissect the mechanism of inhibition and structural features that are important for the selective binding of compound 1. Using a subunit exchange assay, we found that the inhibitor strongly modulates dynamic interactions between IN subunits. Restricting such interactions does not directly interfere with IN binding to DNA substrates or cellular cofactor lens epithelium-derived growth factor, but it compromises the formation of the fully functional nucleoprotein complex. Studies comparing compound 1 with a structurally related IN inhibitor, the tetra-acetylated-chicoric acid derivative (2R,3R)-2,3-bis[[(2E)-3-[3,4-bis(acetyloxy)phenyl]-1-oxo-2-propen-1-yl]oxy]-butanedioic acid (compound 2), indicated striking mechanistic differences between these agents. The structures of the two inhibitors differ only in their central linker regions, with compounds 1 and 2 containing a single methyl ester group and two carboxylic acids, respectively. MS experiments highlighted the importance of these structural differences for selective binding of compound 1 to the IN dimer interface. Moreover, molecular modeling of compound 1 complexed to IN identified a potential inhibitor binding cavity and provided structural clues regarding a possible role of the central methyl ester group in establishing an extensive hydrogen bonding network with both interacting subunits. The proposed mechanism of action and binding site for the small-molecule inhibitor identified in the present study provide an attractive venue for developing allosteric inhibitors of HIV-1 IN

Fibronectin as a Prognostic Indicator in Portal Hypertension

Plasma fibronectin levels were measured in 33 patients with portal hypertension and c6mpared with modified Child’s grading and a previously described prognostic index. Outcome at one year from blood sampling was recorded. Mean plasma fibronectin level was 304.1 mg/ml (sem 24.3) and significantly lower levels were found in patients who had had a variceal bleed within the previous seven days. Plasma fibronectin levels tended to be lower in patients with poor liver function as assessed by modified Child’s grading but this did not achieve statistical significance. Plasma fibronectin alone was not an accurate predictor of one year survival in these patients but only one of seven patients who had a plasma fibronectin level below 300mg/l in association with a poor prognostic index survived for one year

HIV-1 Integrase-DNA Recognition Mechanisms

Integration of a reverse transcribed DNA copy of the HIV viral genome into the host chromosome is essential for virus replication. This process is catalyzed by the virally encoded protein integrase. The catalytic activities, which involve DNA cutting and joining steps, have been recapitulated in vitro using recombinant integrase and synthetic DNA substrates. Biochemical and biophysical studies of these model reactions have been pivotal in advancing our understanding of mechanistic details for how IN interacts with viral and target DNAs, and are the focus of the present review

Quantum Information Processing with Ferroelectrically Coupled Quantum Dots

I describe a proposal to construct a quantum information processor using ferroelectrically coupled Ge/Si quantum dots. The spin of single electrons form the fundamental qubits. Small (<10 nm diameter) Ge quantum dots are optically excited to create spin polarized electrons in Si. The static polarization of an epitaxial ferroelectric thin film confines electrons laterally in the semiconductor; spin interactions between nearest neighbor electrons are mediated by the nonlinear process of optical rectification. Single qubit operations are achieved through "g-factor engineering" in the Ge/Si structures; spin-spin interactions occur through Heisenberg exchange, controlled by ferroelectric gates. A method for reading out the final state, while required for quantum computing, is not described; electronic approaches involving single electron transistors may prove fruitful in satisfying this requirement.Comment: 10 pages, 3 figure

Scanning Angle Plasmon Waveguide Resonance Raman Spectroscopy for the Analysis of Thin Polystyrene Films

Scanning angle (SA) Raman spectroscopy was used to characterize thin polymer films at a sapphire/50 nm gold film/polystyrene/air interface. When the polymer thickness is greater than ∼260 nm, this interface behaves as a plasmon waveguide; Raman scatter is greatly enhanced with both p- and s-polarized excitation compared to an interface without the gold film. In this study, the reflected light intensities from the interface and Raman spectra were collected as a function of incident angle for three samples with different polystyrene thicknesses. The Raman peak areas were well modeled with the calculated mean-square electric field (MSEF) integrated over the polymer film at varying incident angles. A 412 nm polystyrene plasmon waveguide generated 3.34× the Raman signal at 40.52° (the plasmon waveguide resonance angle) compared to the signal measured at 70.4° (the surface plasmon resonance angle). None of the studied polystyrene plasmon waveguides produced detectable Raman scatter using a 180° backscatter collection geometry, demonstrating the sensitivity of the SA Raman technique. The data highlight the ability to measure polymer thickness, chemical content, and, when combined with calculations of MSEF as a function of distance from the interface, details of polymer structure and order. The SA Raman spectroscopy thickness measurements agreed with those obtained from optical interferometery with an average difference of 2.6%. This technique has the potential to impact the rapidly developing technologies utilizing metal/polymer films for energy storage and electronic devices

Low Velocity Ionized Winds from Regions Around Young O Stars

We have observed seven ultracompact HII regions in hydrogen recombination lines in the millimeter band. Toward four of these regions, there is a high velocity (full width to half maximum 60-80 km/s) component in the line profiles. The high velocity gas accounts for 35-70% of the emission measure within the beam. We compare these objects to an additional seven similar sources we have found in the literature. The broad recombination line objects (BRLOs) make up about 30% of all sources in complexes containing ultracompact HII regions. Comparison of spectral line and continuum data implies that the BRLOs coincide with sources with rising spectral indices, >=0.4 up to 100 GHz. Both the number of BRLOs and their frequency of occurrence within HII region complexes, when coupled with their small size and large internal motions, mean that the apparent contradiction between the dynamical and population lifetimes for BRLOs is even more severe than for ultracompact HII regions. We evaluate a number of models for the origin of the broad recombination line emission. The lifetime, morphology, and rising spectral index of the sources argue for photo- evaporated disks as the cause for BRLOs. Existing models for such regions, however, do not account for the large amounts of gas observed at supersonic velocities.Comment: 36 pages, 8 figure

Faraday Rotation as a diagnostic of Galactic foreground contamination of CMB maps

The contribution from the residuals of the foreground can have a significant impact on the temperature maps of the Cosmic Microwave Background (CMB). Mostly, the focus has been on the galactic plane, when foreground cleaning has taken place. However, in this paper, we will investigate the possible foreground contamination, from sources outside the galactic plane in the CMB maps. We will analyze the correlation between the Faraday rotation map and the CMB temperature map. The Faraday rotation map is dependent on the galactic magnetic field, as well as the thermal electron density, and both may contribute to the CMB temperature. We find that the standard deviation for the mean cross correlation deviate from that of simulations at the 99.9% level. Additionally, a comparison between the CMB temperature extrema and the extremum points of the Faraday rotation is also performed, showing a general overlap between the two. Also we find that the CMB Cold Spot is located at an area of strong negative cross correlation, meaning that it may be explained by a galactic origin. Further, we investigate nearby supernova remnants in the galaxy, traced by the galactic radio loops. These super nova remnants are located at high and low galactic latitude, and thus well outside the galactic plane. We find some correlation between the Faraday Rotation and the CMB temperature, at select radio loops. This indicate, that the galactic foregrounds may affect the CMB, at high galactic latitudesComment: 13 pages, 22 figures, 6 table

Mid-infrared interferometry of the massive young stellar object NGC3603 - IRS 9A

We present observations and models for one of these MYSO candidates, NGC3603 IRS 9A. Our goal is to investigate with infrared interferometry the structure of IRS 9A on scales as small as 200AU, exploiting the fact that a cluster of O and B stars has blown away much of the obscuring foreground dust and gas. Observations in the N-band were carried out with the MIDI beam combiner attached to the VLTI. Additional interferometric observations which probe the structure of IRS 9A on larger scales were performed with an aperture mask installed in the T-ReCS instrument of Gemini South. The spectral energy distribution (SED) is constrained by the MIDI N-band spectrum and by data from the Spitzer Space Telescope. Our efforts to model the structure and SED of IRS 9A range from simple geometrical models of the brightness distribution to one- and two-dimensional radiative transfer computations. The target is resolved by T-ReCS, with an equivalent (elliptical) Gaussian width of 330mas by 280mas (2300 AU by 2000 AU). Despite this fact, a warm compact unresolved component was detected by MIDI which is possibly associated with the inner regions of a flattened dust distribution. Based on our interferometric data, no sign of multiplicity was found on scales between about 200AU and 700AU projected separation. A geometric model consisting of a warm (1000 K) ring (400 AU diameter) and a cool (140 K) large envelope provides a good fit to the data. No single model fitting all visibility and photometric data could be found, with disk models performing better than spherical models. While the data are clearly inconsistent with a spherical dust distribution they are insufficient to prove the existence of a disk but rather hint at a more complex dust distribution.Comment: 8 pages, 11 figures. Accepted for publication in A&