Conservation and specialization in PAS domain dynamics

The PAS (Per-ARNT-Sim) superfamily is presented as a well-suited study case to demonstrate how comparison of functional motions among distant homologous proteins with conserved fold characteristics may give insight into their functional specialization. Based on the importance of structural flexibility of the receptive structures in anticipating the signal-induced conformational changes of these sensory systems, the dynamics of these structures were analysed. Molecular dynamics was proved to be an effective method to obtain a reliable picture of the dynamics of the crystal structures of HERG, phy3, PYP and FixL, provided that an extensive conformational space sampling is performed. Other reliable sources of dynamic information were the ensembles of NMR structures of hPASK, HIF-2α and PYP. Essential dynamics analysis was successfully employed to extract the relevant information from the sampled conformational spaces. Comparison of motion patterns in the essential subspaces, based on the structural alignment, allowed identification of the specialized region in each domain. This appears to be evolved in the superfamily by following a specific trend, that also suggests the presence of a limited number of general solutions adopted by the PAS domains to sense external signals. These findings may give insight into unknown mechanisms of PAS domains and guide further experimental studies. © The Author 2005. Published by Oxford University Press. All rights reserved

Predicting the accuracy of protein-ligand docking on homology models

Ligand-protein docking is increasingly used in Drug Discovery. The initial limitations imposed by a reduced availability of target protein structures have been overcome by the use of theoretical models, especially those derived by homology modeling techniques. While this greatly extended the use of docking simulations, it also introduced the need for general and robust criteria to estimate the reliability of docking results given the model quality. To this end, a large-scale experiment was performed on a diverse set including experimental structures and homology models for a group of representative ligand-protein complexes. A wide spectrum of model quality was sampled using templates at different evolutionary distances and different strategies for target-template alignment and modeling. The obtained models were scored by a selection of the most used model quality indices. The binding geometries were generated using AutoDock, one of the most common docking programs. An important result of this study is that indeed quantitative and robust correlations exist between the accuracy of docking results and the model quality, especially in the binding site. Moreover, state-of-the-art indices for model quality assessment are already an effective tool for an a priori prediction of the accuracy of docking experiments in the context of groups of proteins with conserved structural characteristics.Contract/grant sponsor: National Institutes of Health; contract/grant numbers: ES00768

QCD, monopoles on the Lattice and gauge invariance

The number and the location of the monopoles observed on the lattice in QCD configurations happens to depend strongly on the choice of the gauge used to expose them, in contrast to the physical expectation that monopoles be gauge invariant objects. It is proved by use of the non abelian Bianchi identities (NABI) that monopoles are indeed gauge invariant, but the method used to detect them depends, in a controllable way, on the choice of the abelian projection. Numerical checks are presented.Comment: 3 pages, 1 figure. Presented at the Conference QUARK CONFINEMENT AND THE HADRON SPECTRUM IX, Madrid Aug.30-Sept.3 201

On the phase diagram of the Higgs SU(2) model

The Higgs SU(2) model with fixed Higgs length is usually believed to have two different phases at high gauge coupling (\beta), separated by a line of first order transitions but not distinuguished by any typical symmetry associated with a local order parameter, as first proved by Fradkin and Shenker. We show that in regions of the parameter space where it is usually supposed to be a first order phase transition only a smooth crossover is in fact present.Comment: 6 pages, 6 figures. Talk presented at The XXVI International Symposium on Lattice Field Theory, July 14 - 19, 2008 - Williamsburg, Virginia, US

Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis

The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that is activated by a structurally diverse array of synthetic and natural chemicals, including toxic halogenated aromatic hydrocarbons such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Analysis of the occurring in the AhR ligand binding and activation processes requires structural information on the AhR Per-Arnt-Sim (PAS) B-containing ligand binding domain, for which no experimentally determined structure has been reported. With the availability of extensive structural information on homologous PAS-containing proteins, a reliable model of the mouse AhR PAS B domain was developed by comparative modeling techniques. The PAS domain structures of the functionally related hypoxia-inducible factor 2α (HIF-2α) and AhR nuclear translocator (ARNT) proteins, which exhibit the highest degree of sequence identity and similarity with AhR, were chosen to develop a two-template model. To confirm the features of the modeled domain, the effects of point mutations in selected residue positions on both TCDD binding to the AhR and TCDD-dependent transformation and DNA binding were analyzed. Mutagenesis and functional analysis results are consistent with the proposed model and confirm that the cavity modeled in the interior of the domain is indeed involved in ligand binding. Moreover, the physicochemical characteristics of some residues and of their mutants, along with the effects of mutagenesis on TCDD and DNA binding, also suggest some key features that are required for ligand binding and activation of mAhR at a molecular level, thus providing a framework for further studies. © 2007 American Chemical Society

A test of first order scaling in Nf =2 QCD: a progress report

We present the status of our analysis on the order of the finite temperature transition in QCD with two flavors of degenerate fermions. Our new simulations on large lattices support the hypothesis of the first order nature of the transition, showing a preliminary two state signal. We will discuss the implications and the next steps in our analysis.Comment: 6 pages, 4 figures. Talk presented at The XXVI International Symposium on Lattice Field Theory, July 14 - 19, 2008 - Williamsburg, Virginia, US

Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis

The aryl hydrocarbon receptor (AhR) is a ligand-dependent, basic helix-loop-helix Per-Arnt-Sim (PAS)-containing transcription factor that can bind and be activated by structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Our previous three-dimensional homology model of the mouse AhR (mAhR) PAS B ligand binding domain allowed identification of the binding site and its experimental validation. We have extended this analysis by conducting comparative structural modeling studies of the ligand binding domains of six additional highaffinity mammalian AhRs. These results, coupled with site-directed mutagenesis and AhR functional analysis, have allowed detection of the "TCDD binding-fingerprint" of conserved residues within the ligand binding cavity necessary for high-affinity TCDD binding and TCDD-dependent AhR transformation DNA binding. The essential role of selected residues was further evaluated using molecular docking simulations of TCDD with both wild-type and mutant mAhRs. Taken together, our results dramatically improve our understanding of the molecular determinants of TCDD binding and provide a basis for future studies directed toward rationalizing the observed species differences in AhR sensitivity to TCDD and understanding the mechanistic basis for the dramatic diversity in AhR ligand structure. © 2009 American Chemical Society

Phase diagram of the lattice SU(2) Higgs model

We perform a detailed study of the phase diagram of the lattice Higgs SU(2) model with fixed Higgs field length. Consistently with previsions based on the Fradkin Shenker theorem we find a first order transition line with an endpoint whose position we determined. The diagram also shows cross-over lines: the cross-over corresponding to the pure SU(2) bulk is also present at nonzero coupling with the Higgs field and merges with the one that continues the line of first order transition beyond the critical endpoint. At high temperature the first order line becomes a crossover, whose position moves by varying the temperature.Comment: 18 pages, 15 figure

Experimental results of a national technical assessment procedure on commercial FRP for structural strengthening: wet-lay-up systems

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The disorder parameter of dual superconductivity in QCD revisited

We discover the origin of the pathologies of the disorder parameter used in previous papers to detect dual superconductivity of QCD vacuum, and we remove them by defining an improved disorder parameter. A check of the approach is made by numerical simulations of SU(2) gauge theory, which demonstrate that the approach is consistent and with it that deconfinement is a transition from dual superconductor to normal.Comment: 13 pages, 12 eps figure