The DEAD-box helicase DDX3X is a critical component of the TANK-binding kinase 1-dependent innate immune response

TANK-binding kinase 1 (TBK1) is of central importance for the induction of type-I interferon (IFN) in response to pathogens. We identified the DEAD-box helicase DDX3X as an interaction partner of TBK1. TBK1 and DDX3X acted synergistically in their ability to stimulate the IFN promoter, whereas RNAi-mediated reduction of DDX3X expression led to an impairment of IFN production. Chromatin immunoprecipitation indicated that DDX3X is recruited to the IFN promoter upon infection with Listeria monocytogenes, suggesting a transcriptional mechanism of action. DDX3X was found to be a TBK1 substrate in vitro and in vivo. Phosphorylation-deficient mutants of DDX3X failed to synergize with TBK1 in their ability to stimulate the IFN promoter. Overall, our data imply that DDX3X is a critical effector of TBK1 that is necessary for type I IFN induction

Sodium ion interactions with aqueous glucose: Insights from quantum mechanics, molecular dynamics, and experiment

In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on B-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of α-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na + suggests that computational studies of glucose reactions in the presence of inorganic salts need to ensure thorough sampling of the cation positions, in addition to sampling glucose rotamers. The effect of NaCl on the relative populations of the anomers is experimentally quantified with light polarimetry. These results support the computational findings that Na + interacts similarly with a- and B-glucose

Bacteria Modulate the CD8+ T Cell Epitope Repertoire of Host Cytosol-Exposed Proteins to Manipulate the Host Immune Response

The main adaptive immune response to bacteria is mediated by B cells and CD4+ T-cells. However, some bacterial proteins reach the cytosol of host cells and are exposed to the host CD8+ T-cells response. Both gram-negative and gram-positive bacteria can translocate proteins to the cytosol through type III and IV secretion and ESX-1 systems, respectively. The translocated proteins are often essential for the bacterium survival. Once injected, these proteins can be degraded and presented on MHC-I molecules to CD8+ T-cells. The CD8+ T-cells, in turn, can induce cell death and destroy the bacteria's habitat. In viruses, escape mutations arise to avoid this detection. The accumulation of escape mutations in bacteria has never been systematically studied. We show for the first time that such mutations are systematically present in most bacteria tested. We combine multiple bioinformatic algorithms to compute CD8+ T-cell epitope libraries of bacteria with secretion systems that translocate proteins to the host cytosol. In all bacteria tested, proteins not translocated to the cytosol show no escape mutations in their CD8+ T-cell epitopes. However, proteins translocated to the cytosol show clear escape mutations and have low epitope densities for most tested HLA alleles. The low epitope densities suggest that bacteria, like viruses, are evolutionarily selected to ensure their survival in the presence of CD8+ T-cells. In contrast with most other translocated proteins examined, Pseudomonas aeruginosa's ExoU, which ultimately induces host cell death, was found to have high epitope density. This finding suggests a novel mechanism for the manipulation of CD8+ T-cells by pathogens. The ExoU effector may have evolved to maintain high epitope density enabling it to efficiently induce CD8+ T-cell mediated cell death. These results were tested using multiple epitope prediction algorithms, and were found to be consistent for most proteins tested

Bioinformatics and molecular modeling in glycobiology

The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein–carbohydrate interaction are reviewed

Experimental and theoretical investigation of the A 3Pi - X 3Sigma- transition of NH/D-Ne

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THEORETICAL ANALYSIS OF THE A3Π−X3Σ−A^{3}\Pi-X^{3}\Sigma^{-} BANDS OF NH/D-Ne

Author Institution: Department of Chemistry, Emory UniversityRotationally resolved bands of NH/D-Ne have been observed in association with the $A^{3}\Pi-X^{3}\Sigma^{-} 1-0$ and $0-0$ transitions of NH/D. To guide the analysis of the spectra for the complex we have used high-level theoretical methods to calculate potential energy surfaces for the X and A states. The ground state surface has a well depth of $40 cm^{-1}$ and a linear NH-Ne equilibrium structure. The bending potential is predicted to be very shallow, so the zero-point level of the complex is expected to exhibit a large amplitude bending motion. The potential surface for the A state is more deeply bound $(D_{e}=90 cm^{-1})$ and anisotropic. The global minimum is for linear NH-Ne, but there is a secondary minimum for linear Ne-NH with a well depth of $45 cm^{-1}$. Ro-vibronic levels of NH/D(A)-Ne were calculated from the potentials by numerical solution of the close-coupled equations. The results were in reasonably good agreement with the observed energy level structure. With one exception the bands that exhibited sharp rotational structure could be assigned to levels that correlate with the $NH/D(A^{3}\Pi_{2})-Ne$ spinorbit component. A single sharp feature was assigned to $NH/D(A^{3}\Pi_{1})-Ne$. Details of the calculations and a discussion of the assignments for the observed levels will be presented

Electronic Spectroscopy and Dynamics of the CH/D-Ne Van der Waals Complexes

1) W. H. Basinger, U. Schnupf, and M. C. Heaven, {Electronic Spectroscopy and Dynamics Of the CHID-Ne Van der Waals Complex}. Submitted to: Faraday Discussion No. 97. Structure and Dynamics of Van der Waals Complexes. 2) G. W. Lemire, M. J. Mcquaid, A. J. Kotlar, and R. C. Sausa, J. Chem. Phys., 1993, 99, 91.Author Institution: Department of Chemistry, Emory UniversityRotationally resolved spectra for the $A^{2}\Delta -X^{2} \Pi$ and $B^{2}\Sigma -X^{2} \Pi$ transitions of $CH/D-Ne^{1}$ have been recorded. Bands of both the A-X and B-X complexes were observed in association with the monomer 0-0 transition. In addition, complex bands associated with B-X monomer 1-0 transition were also recorded. Analyses of the ro-vibronic structures show that the complex is weakly bound in both the ground (X) and excited (A,B) electronic states. Preliminary results from the analysis of the highly congested A-X bands indicate that intermolecular bond length is unchanged upon excitation. A more detailed analysis is in progress and will be addressed. Analysis of the bands in the B-X system indicate that excitation to the B state reduces the binding energy and lengthens the intermolecular bond. The rotational levels of the X state were characterized by half-integer quantum numbers. This is in contrast to the situation for $CH(X)-Ar^{2}$ where the ground state exhibits integer rotational quantum numbers. The n=2 and n=1, k=0 bands in the B-X system showed homogeneous line broading as a result of rotational predissociation of the CH-Ne complex. B-X complex band assignments, rotational constants, and predissociation lifetimes will be discussed. Calculations are currently in progress on A-X system of CH/D-Ne in order to elucidate the origins of the rich rotational contours observed. Details and progress of the calculation will be reported on