In silico design of peptidic inhibitors targeting estrogen receptor alpha dimer interface

Human estrogen receptor alpha (ERα), which acts as a biomarker and as a therapeutic target for breast cancers, is activated by agonist ligands and co-activator proteins. Selective estrogen receptor modulators (SERM) act as antagonists in specific tissues and tamoxifen, a SERM, has served as a drug for decades for ERα-positive breast cancers. However, the ligand-selective and tissue-specific response of ERα biological activity and the resistance to tamoxifen treatment in advanced stages of ERα-positive breast cancers underscores the need to find a ligand-independent inhibitor for ERα. Here we present a ligand-independent approach of inhibiting ERα transactivation targeting its dimerization-a key process of ERα biological activity. Using in silico techniques, we first elucidated the hydrogen bond interactions involved in dimerization and identified three interfacial sequence motifs, where sequence I (DKITD) and sequence II (QQQHQRLAQ) of one monomer form hydrogen bonding with sequence II and sequence I of the second monomer, respectively, and sequence III (LSHIRHMSNK) hydrogen bonds with the same from the second monomer. Studying the structural stability and the binding affinity of the peptides derived from these sequence motifs, we found that an extended and ARG mutated version (LQQQHQQLAQ) of sequence II can act as a suitable template for designing peptidic inhibitors. It provides additional structural stability and interacts more strongly with ERα dimer interface groove formed by helices 9 and 10/11 and prevent ERα dimerization. Our result provides a novel therapeutic designing pipeline for ligand-independent inhibition of ERα.     

Spherically symmetric inhomogeneous dust collapse in higher dimensional space-time and cosmic censorship hypothesis

We consider a collapsing spherically symmetric inhomogeneous dust cloud in higher dimensional space-time. We show that the central singularity of collapse can be a strong curvature or a weak curvature naked singularity depending on the initial density distribution.     

<Emphasis Type="Italic">In-silico</Emphasis> Screening using Flexible Ligand Binding Pockets: A Molecular Dynamics-based Approach

Summary In-silico screening of flexible ligands against flexible ligand binding pockets (LBP) is an emerging approach in structure-based drug discovery. Here, we describe a molecular dynamics (MD) based docking approach to investigate the influence on the high-throughput in-silico screening of small molecules against flexible ligand binding pockets. In our approach, an ensemble of 51 energetically favorable structures of the LBP of human estrogen receptor α (hERα) were collected from 3 ns MD simulations. In-silico screening of 3500 endocrine disrupting compounds against these flexible ligand binding pockets resulted in thousands of ER–ligand complexes of which 582 compounds were unique. Detailed analysis of MD generated structures showed that only 17 of the LBP residues significantly contribute to the overall binding pocket flexibility. Using the flexible LBP conformations generated, we have identified 32 compounds that bind better to the flexible ligand-binding pockets compared to the crystal structure. These compounds, though chemically divergent, are structurally similar to the natural hormone. Our MD-based approach in conjunction with grid–based distributed computing could be applied routinely for in-silico screening of large databases against any given target.     

Scattering by small defects in the neighbourhood of a fluid-solid interface

The scattering of incident plane elastic waves by a varietyof different defects that lie upon a fluid-solid interface isconsidered here using matched asymptotic expansions. The expansionscheme is developed in terms of a parameter , the ratio of typicaldefect length scale to a typical wavelength of the incidentfield, taken to be small. Three different canonical situations occur and these are illustratedvia three specific examples treated here: a rigid strut, anedge crack, and a rigid strip. In each case the leading-ordermatching is performed to identify the leading-order contributionof the defect to the acoustic field in the far field. In particular,each defect is identified with a source of dipole response ininterfacial stress of displacement. It is shown in the limit as s<<s1 that in the inner problemsthe fluid and solid pieces uncouple in a particularly convenientmanner allowing analytical solutions to be deduced. These arethen matched with appropriate outer solutions.     

Ion-pair assisted recovery of matrix-assisted laser desorption/ionization mass spectral signals from SDS-containing peptide-protein mixtures

We have developed a simple and effective means of using alkylammonium ion-pairing agents, such as cetyltetramethylammonium bromide, to recover matrix assisted laser desorption/ionization mass spectrometric (MALDI-MS) signals from sodium dodecyl sulfate (SDS)-containing protein and peptide samples. A two-layer method of matrix preparation, with a bottom matrix layer of ion-pairing agents and a top matrix layer of SDS protein samples, is essential for reproducible MALDI mass spectra with good recovery. Both buffer ions and ion-pairing agents have profound effects on signal recovery and can be rapidly and systematically optimized. This practical technique, termed ion-pair assisted recovery (IPAR), is compatible with major SDS-based biotechniques and can be easily incorporated into high-throughput proteomic analysis.     

On a Simple Nonisothermal Adsorption Experiment with Organic Vapors and an Inertial Microbalance To Study the Surface Properties of Hybrid (Organic/Inorganic) Porous Materials

A nonisothermal adsorption experiment using a controlled flow of cyclopentane in the 333-313 K range is used to simultaneously estimate the specific surface area and micropore volume of a hybrid (organic/inorganic) alcogel. For reference, the method is also applied to an all-inorganic material with a more rigid structure, namely, a high surface area SiO(2)-Al(2)O(3). The proposed data analysis provides guidelines to determine whether adsorption data on a certain adsorbate/adsorbent system can be modeled effectively as a convolution of BET (meso- and macropore) and Dubinin-Radushkevitch (DR, micropore) contributions. Copyright 2000 Academic Press.     

Meson production in p + d reactions

Total and differential cross sections for the reactions p + d → ³He + m ⁰ with m=π, η and p + d → ³H+π⁺ were measured with the GEM detector at COSY for beam momenta between threshold and the maximum of the corresponding baryon resonance. For both reactions a strong forward-backward asymmetry was found. The data were compared with model calculations. The aspect of isospin symmetry breaking is studied. Representing the GEM Collaboration     

Working group report: Heavy-ion physics and quark-gluon plasma

This is the report of Heavy Ion Physics and Quark-Gluon Plasma at WHEPP-09 which was part of Working Group-4. Discussion and work on some aspects of quark-gluon plasma believed to have created in heavy-ion collisions and in early Universe are reported.     

Interaction between explosive and analyte layers in explosive matrix-assisted plasma desorption mass spectrometry

An HMX/insulin two-layer system was chosen as a model for further investigation of the matrix properties of explosive materials for protein analytes in plasma desorption mass spectrometry. The dependencies of the molecular ion yield and average charge state as a function of the analyte thickness were studied. An increase in the charge state of multiply protonated molecular species was confirmed as the major matrix effect, with the average charge state z at the smallest thickness studied being higher than in matrix-assisted laser desorption/ionization and closer to the value obtained in electrospray ionization under standard acidic conditions. Observed charge state distributions are significantly narrower than the corresponding Poisson distributions, which suggests that the protonation of insulin is limited in plasma desorption by the number of basic sites in the molecule, similar to electrospray ionization. Both the curve displaying total molecular ion yield and the one showing the total charge (proton) yield as a function of the insulin thickness have maxima at a thickness different from an insulin monolayer. These observations diminish the significance of a matrix/analyte interface mechanism for the explosive matrix assistance. Instead, a mechanism related to the chemical energy release during conversion of the explosive after the ion impact is proposed. As additional mechanisms, enhanced protonation of the analyte through collisions with products of the explosive decay is considered, as well as electron scavenging by other products, which leads to a higher survival probability of positively charged protein molecular ions. Copyright 1999 John Wiley & Sons, Ltd.     

Quantum chromodynamics: Working group report

This is the report of the QCD working group at WHEPP-6. Discussions and work on heavy ion collisions, polarized scattering, and collider phenomenology are reported.