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Abstract: The archaeal RNA polymerase (RNAP) shares structural similarities with eukaryotic RNAP II but requires a reduced subset of general transcription factors for promoter-dependent initiation. To deepen our knowledge of cellular transcription, we have determined the structure of the 13-subunit DNA-directed RNAP from Sulfolobus shibatae at 3.35 Å resolution. The structure contains the full complement of subunits, including RpoG/Rpb8 and the equivalent of the clamp-head and jaw domains of the eukaryotic Rpb1. Furthermore, we have identified subunit Rpo13, an RNAP component in the order Sulfolobales, which contains a helix-turn-helix motif that interacts with the RpoH/Rpb5 and RpoA'/Rpb1 subunits. Its location and topology suggest a role in the formation of the transcription bubble.

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Abstract: Cardiovascular stents are commonly made from 316L stainless steel and are deployed within stenosed arterial lesions using balloon expansion. Deployment involves inflating the balloon and plastically deforming the stent until the required diameter is obtained. This plastic deformation induces static stresses in the stent, which will remain for the lifetime of the device. In order to determine these stresses, finite element models of the unit cells of geometrically different, commercially available balloon expandable stents have been created, and deployment and elastic recoil have been simulated. In this work the residual stresses associated with deployment and recoil are compared for the various stent geometries, with a view to establishing appropriate initial stress states for fatigue loading for the stents. The maximum, minimum, and mean stresses induced in the stent due to systolic/diastolic pressure are evaluated, as are performance measures such as radial and longitudinal recoil.

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Abstract: LysR-type transcriptional regulators (LTTRs) form the largest family of bacterial regulators acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes. The LTTR, CrgA, from the human pathogen Neisseria meningitidis, is upregulated during bacterial-host cell contact. Here, we report the crystal structures of both regulatory domain and full-length CrgA, the first of a novel subclass of LTTRs that form octameric rings. Non-denaturing mass spectrometry analysis and analytical ultracentrifugation established that the octameric form of CrgA is the predominant species in solution in both the presence and absence of an oligonucleotide encompassing the CrgA-binding sequence. Furthermore, analysis of the isolated CrgA-DNA complex by mass spectrometry showed stabilization of a double octamer species upon DNA binding. Based on the observed structure and the mass spectrometry findings, a model is proposed in which a hexadecameric array of two CrgA oligomers binds to its DNA target site.

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Abstract: Experimental and computational searches for the crystal structures of the five commercially available isomers of dichloronitrobenzene and 3,4-dinitrochlorobenzene were performed to assess the relationship between functional group interactions and steric requirements in determining the solid forms. Experimentally, this resulted in the first crystal structure determination of 2,4-dichloronitrobenzene, two solvates of 3,4-dichloronitrobenzene and one of 3,4-dinitrochlorobenzene. Additionally, low temperature redeterminations of the crystal structures were obtained for 2,5-dichloronitrobenzene, 3,4-dichloronitrobenzene, and both the ?- and ?-forms of 3,4-dinitrochlorobenzene. The searches for energetically feasible structures of each of these compounds showed a wide variety of distributions leading to varying degrees of clarity of prediction of the solid state behavior. These range from 2,3-dichloronitrobenzene, which only adopts the crystal structure that was clearly the most thermodynamically stable of all five isomers, through complex systems, which show a range of low energy minima indicating possible polymorphism and solvate formation, to 2,4-dichloronitrobenzene, which can conformationally distort and adopts a complicated Z? = 2 crystal structure.

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Abstract: Background: Despite the existence of over 50 subtypes and circulating recombinant forms of HIV-1, Subtype C dominates the heterosexual pandemic causing approximately 56% of all infections.Objective: To evaluate whether viral genetic factors may contribute to the observed subtype-C predominance.Methods: Chimeric viruses were generated using V1-V3 envelope fragments from a subtype-A/C dually infected woman with preferential genital replication of subtype C. Viral adaptation, spread and cell fusion ability were evaluated in vitro using peripheral blood mononuclear cells and HeLa-CD4-CCR5 cell lines, sequencing and cloning. Structural modeling was performed using a crystal structure of gp120-CD4-X5. Phylogenetic analysis was done using subtype-A, subtype-B and subtype-C sequences from blood and cervix of 37 infected women and database sequences.Results: We identified two envelope motifs, compact V1-V2 loops and V3-316T, which are found at high frequency throughout subtype-C evolution and affect gp120 interactions with CD4 and CCR5, respectively. When a V1-Delta 5 deletion or V3-A316T was incorporated into subtype A, each increased viral fusion and spread several fold in peripheral blood mononuclear cell and cell lines with low CCR5 expression. Structural modeling suggested the formation of an additional hydrogen bond between V3 and CCR5. Moreover, we found preferential selection of HIV with 316T and/or extremely short V1-V2 loops in cervices of three women infected with subtypes A/C, B or C.Conclusion: As CD(4+)-CCR(5+)-T cells are key targets for genital HIV infection and cervical selection can favor compact V1-V2 loops and 316T, which increase viral infectivity, we propose that these conserved subtype-C motifs may contribute to transmission and spread of this subtype. (C) 2009 Wolters Kluwer Health vertical bar Lippincotl Williams & Wilkins