Molecular Dynamics of HIV1-Integrase in Complex with 93del - A Structural Perspective on the Mechanism of Inhibition

HIV1 integrase is an important target for the antiviral therapy. Guanine-rich quadruplex, such as 93del, have been shown to be potent inhibitors of this enzyme and thus representing a new class of antiviral agents. Although X-ray and NMR structures of HIV1 integrase and 93del have been reported, there is no structural information of the complex and the mechanism of inhibition still remains unexplored. A number of computational methods including automated protein-DNA docking and molecular dynamics simulation in explicit solvent were used to model the binding of 93del to HIV1 integrase. Analysis of the dynamic behaviour of the complex using principal components analysis and elastic network modelling techniques allow us to understand how the binding of 93del aptamer and its interactions with key residues affect the intrinsic motions of the catalytic loops by stabilising them in catalytically inactive conformations. Such insights into the structural mechanism of inhibition can aid in improving the design of anti-HIV aptamers.

Dynamic oscillation of translation and stress granule formation mark the cellular response to virus infection

Virus infection-induced global protein synthesis suppression is linked to assembly of stress granules (SGs), cytosolic aggregates of stalled translation preinitiation complexes. To study long-term stress responses, we developed an imaging approach for extended observation and analysis of SG dynamics during persistent hepatitis C virus (HCV) infection. In combination with type 1 interferon, HCV infection induces highly dynamic assembly/disassembly of cytoplasmic SGs, concomitant with phases of active and stalled translation, delayed cell division, and prolonged cell survival. Double-stranded RNA (dsRNA), independent of viral replication, is sufficient to trigger these oscillations. Translation initiation factor eIF2a phosphorylation by protein kinase R mediates SG formation and translation arrest. This is antagonized by the upregulation of GADD34, the regulatory subunit of protein phosphatase 1 dephosphorylating eIF2a. Stress response oscillation is a general mechanism to prevent long-lasting translation repression and a conserved host cell reaction to multiple RNA viruses, which HCV may exploit to establish persistence.

Mechanism of gas permeation in processed HNBR/nanoclay composites

The influence of the layered silicate clay platelets on the nitrogen permeation properties of hydrogenated nitrile butadiene rubber (HNBR)/nanoclay nanocomposites has been investigated. Nanocomposites of HNBR modified with different percentages of the organoclay are processed through various routes. Commercially available organoclay (CLOISITE 15A) and various silane-coupling agents are used to improve the dispersion of the nanoclay in HNBR. A total of 10 different formulations of nanocomposites are manufactured. The addition of the organoclay has resulted in a significant enhancement of the nitrogen barrier properties of the manufactured nanocomposite. The mechanism of the reduction in the permeability is explained through the changes in the morphology and its bond to the filler. These changes are confirmed through examination of the morphology using x-ray diffraction, transmission electron microscope, and dynamic mechanical thermal analysis. There has been a drastic reduction up to 55.7% in nitrogen permeability. The reduction in gas permeation in HNBR is attributed to uniformly exfoliated clay platelets. Finally, three different permeability models, namely, the Nielsen model, modified Nielsen model, and Cussler model, have also been considered to predict the permeability behavior of nanocomposites with different volume filler fractions. The experimental values of gas permeability have been compared with theoretical models. It is observed that the modified Nielsen model closely matches with the measured permeation behavior. © 2011 Wiley Periodicals, Inc.

Fast Byzantine Leader Election in Dynamic Networks

We study the fundamental Byzantine leader election problem in dynamic networks where the topology can change from round to round and nodes can also experience heavy {\em churn} (i.e., nodes can join and leave the network continuously over time). We assume the full information model where the Byzantine nodes have complete knowledge about the entire state of the network at every round (including random choices made by all the nodes), have unbounded computational power and can deviate arbitrarily from the protocol. The churn is controlled by an adversary that has complete knowledge and control over which nodes join and leave and at what times and also may rewire the topology in every round and has unlimited computational power, but is oblivious to the random choices made by the algorithm. Our main contribution is an $O(\log^3 n)$ round algorithm that achieves Byzantine leader election under the presence of up to $O({n}^{1/2 - \epsilon})$ Byzantine nodes (for a small constant $\epsilon > 0$) and a churn of up to \\$O(\sqrt{n}/\poly\log(n))$ nodes per round (where $n$ is the stable network size).The algorithm elects a leader with probability at least $1-n^{-\Omega(1)}$ and guarantees that it is an honest node with probability at least $1-n^{-\Omega(1)}$; assuming the algorithm succeeds, the leader's identity will be known to a $1-o(1)$ fraction of the honest nodes. Our algorithm is fully-distributed, lightweight, and is simple to implement. It is also scalable, as it runs in polylogarithmic (in $n$) time and requires nodes to send and receive messages of only polylogarithmic size per round.To the best of our knowledge, our algorithm is the first scalable solution for Byzantine leader election in a dynamic network with a high rate of churn; our protocol can also be used to solve Byzantine agreement in a straightforward way.We also show how to implement an (almost-everywhere) public coin with constant bias in a dynamic network with Byzantine nodes and provide a mechanism for enabling honest nodes to store information reliably in the network, which might be of independent interest.

Strength reduction of till under dynamic pore pressure condition

Cuttings in heavily overconsolidated clays are known to be susceptible to progressive deformation caused by creep and fatigue that usually begins at the toe of the slope. The progressive deformation leads to strength reduction with time at constant stress (or called softening) and could be accelerated by fluctuation of groundwater level associated with more extreme rainfall events predicted through climate change. The purpose of this paper is to assess the mechanism of progressive deformation due to creep and fatigue using element testing on samples of till. The samples were subjected to fully drained loading and the deviator stresses were held constant at various percentages of peak failure stress, while the pore water pressure was kept static or dynamic (fluctuating ±5 kPa) over a period of time. The results have shown that the samples experienced significant deformation even at a higher factor of safety (i.e. the failure deviator stress/deviator stress at which the pore water pressure was fluctuated) under pore water pressure dynamics.

A Molecular Mechanism for Sequential Activation of a G Protein-Coupled Receptor

Ligands targeting G protein-coupled receptors (GPCRs) are currently classified as either orthosteric, allosteric, or dualsteric/bitopic. Here, we introduce a new pharmacological concept for GPCR functional modulation: sequential receptor activation. A hallmark feature of this is a stepwise ligand binding mode with transient activation of a first receptor site followed by sustained activation of a second topographically distinct site. We identify 4-CMTB (2-(4-chlorophenyl)-3-methyl-N-(thiazol-2-yl)butanamide), previously classified as a pure allosteric agonist of the free fatty acid receptor 2, as the first sequential activator and corroborate its two-step activation in living cells by tracking integrated responses with innovative label-free biosensors that visualize multiple signaling inputs in real time. We validate this unique pharmacology with traditional cellular readouts, including mutational and pharmacological perturbations along with computational methods, and propose a kinetic model applicable to the analysis of sequential receptor activation. We envision this form of dynamic agonism as a common principle of nature to spatiotemporally encode cellular information.