Division of the Salmonella-Containing Vacuole and Depletion of Acidic Lysosomes in Salmonella-Infected Host Cells Are Novel Strategies of Salmonella enterica To Avoid Lysosomes

Salmonella has evolved several strategies to counteract intracellular microbicidal agents like reactive oxygen and nitrogen species. However, it is not yet clear how Salmonella escapes lysosomal degradation. Some studies have demonstrated that Salmonella can inhibit phagolysosomal fusion, whereas other reports have shown that the Salmonella-containing vacuole (SCV) fuses/interacts with lysosomes. Here, we have addressed this issue from a different perspective by investigating if the infected host cell has a sufficient quantity of lysosomes to target Salmonella. Our results suggest that SCVs divide along with Salmonella, resulting in a single bacterium per SCV. As a consequence, the SCV load per cell increases with the division of Salmonella inside the host cell. This demands more investment from the host cell to counteract Salmonella. Interestingly, we observed that Salmonella infection decreases the number of acidic lysosomes inside the host cell both in vitro and in vivo. These events potentially result in a condition in which an infected cell is left with insufficient acidic lysosomes to target the increasing number of SCVs, which favors the survival and proliferation of Salmonella inside the host cell.

Complex solitons in Bose-Einstein condensates with two- and three-body interactions

For the first time, we find the complex solitons for a quasi-one-dimensional Bose-Einstein condensate with two-and three-body interactions. These localized solutions are characterized by a power law behaviour. Both dark and right solitons can be excited in the experimentally allowed parameter domain, when two-and three-body interactions are,respectively, repulsive and attractive. The dark solitons travel with a constant speed, which is quite different from the Lieb mode, where profiles with different speeds, bounded above by sound velocity, can exist for specified interaction strengths. We also study the properties of these solitons in the presence of harmonic confinement with time-dependent nonlinearity and loss. The modulational instability and the Vakhitov-Kolokolov criterion of stability are also studied.

MIPS: metal interactions in protein structures

MIPS (metal interactions in protein structures) is a database of metals in the three-dimensional acromolecular structures available in the Protein Data Bank. Bound metal ions in proteins have both catalytic and structural functions. The proposed database serves as an open resource for the analysis and visualization of all metals and their interactions with macromolecular (protein and nucleic acid) structures. MIPS can be searched via a user-friendly interface, and the interactions between metals and protein molecules, and the geometric parameters, can be viewed in both textual and graphical format using the freely available graphics plug-in Jmol. MIPS is updated regularly, by means of programmed scripts to find metal-containing proteins from newly released protein structures. The database is useful for studying the properties of coordination between metals and protein molecules. It also helps to improve understanding of the relationship between macromolecular structure and function. This database is intended to serve the scientific community working in the areas of chemical and structural biology, and is freely available to all users, around the clock, at http://dicsoft2.physics.iisc.ernet.in/mips/.

Phage lambda beta protein, a component of general recombination, is associated with host ribosomal S1 protein

We have purified phage lambda beta protein produced by a recombinant plasmid carrying bet gene and confirm that it forms a complex with a protein of relative molecular mass 70 kDa. Therefore, beta protein, a component of general genetic recombination, is associated with two functionally diverse complexes; one containing exonuclease and the other 70 kDa protein. Using a number of independent methods, we show that 70 kDa protein is the ribosomal S1 protein of E. coli. Further, the association of 70 kDa protein with beta protein is biologically significant, as the former inhibits joining of the terminal ends of lambda chromosome and renaturation of complementary single stranded DNA promoted by the latter. More importantly, these findings initiate an understanding of an important mode of host- virus interaction in general with specific implication(s) in homologous genetic recombination.

Inter-helical Interactions in Membrane Proteins: Analysis Based on the Local Backbone Geometry and the Side Chain Interactions

The availability of a significant number of the Structures of helical membrane proteins has prompted us to investigate the mode of helix-helix packing. In the present study, we have considered a dataset of alpha-helical membrane proteins representing Structures solved from all the known superfamilies. We have described the geometry of all the helical residues in terms of local coordinate axis at the backbone level. Significant inter-helical interactions have been considered as contacts by weighing the number of atom-atom contacts, including all the side-chain atoms. Such a definition of local axis and the contact criterion has allowed us to investigate the inter-helical interaction in a systematic and quantitative manner. We show that a single parameter (designated as alpha), which is derived from the parameters representing the Mutual orientation of local axes, is able to accurately Capture the details of helix-helix interaction. The analysis has been carried Out by dividing the dataset into parallel, anti-parallel, and perpendicular orientation of helices. The study indicates that a specific range of alpha value is preferred for interactions among the anti-parallel helices. Such a preference is also seen among interacting residues of parallel helices, however to a lesser extent. No such preference is seen in the case of perpendicular helices, the contacts that arise mainly due to the interaction Of Surface helices with the end of the trans-membrane helices. The Study Supports the prevailing view that the anti-parallel helices are well packed. However, the interactions between helices of parallel orientation are non-trivial. The packing in alpha-helical membrane proteins, which is systematically and rigorously investigated in this study, may prove to be useful in modeling of helical membrane proteins.

Investigation of inter-ion interactions in N,N,N',N'-tetramethylethylenediammonium dithiocyanate via experimental and theoretical charge density studies

The crystal structure of the N,N,N',N'-tetramethylethylenediammonium dithiocyanate salt has been examined by experimental charge density studies from high-resolution X-ray diffraction data. The corresponding results are compared with multipole refinements, using theoretical structure factors obtained from a periodic density functional theory calculation at the B3LYP level with a 6-31G** basis set. The salt crystallizes in space group P (1) over bar and contains only a single ion pair with an inversion center in the cation. The salt has thus one unique classical N+-H center dot center dot center dot(NCS)(-) hydrogen bond but also has six other weaker interactions: four C-H center dot center dot center dot S, one C-H center dot center dot center dot N, and one C-H center dot center dot center dot C-pi. The nature of all these interactions has been examined topologically using Bader's quantum theory of "atoms in molecules" and all eight of the Koch-Popelier criteria. The experimental and theoretical approaches agree well and both show that the inter-ion interactions, even in this simplest of systems, play an integrated and complex role in the packing of the ions in the crystal. Electrostatic potential maps are derived from experimental charge densities. This is the first time such a system has been examined in detail by these methods.

Electromechanical interactions in a carbon nanotube based thin film field emitting diode

Carbon nanotubes (CNTs) have emerged as promising candidates for biomedical x-ray devices and other applications of field emission. CNTs grown/deposited in a thin film are used as cathodes for field emission. In spite of the good performance of such cathodes, the procedure to estimate the device current is not straightforward and the required insight towards design optimization is not well developed. In this paper, we report an analysis aided by a computational model and experiments by which the process of evolution and self-assembly (reorientation) of CNTs is characterized and the device current is estimated. The modeling approach involves two steps: (i) a phenomenological description of the degradation and fragmentation of CNTs and (ii) a mechanics based modeling of electromechanical interaction among CNTs during field emission. A computational scheme is developed by which the states of CNTs are updated in a time incremental manner. Finally, the device current is obtained by using the Fowler–Nordheim equation for field emission and by integrating the current density over computational cells. A detailed analysis of the results reveals the deflected shapes of the CNTs in an ensemble and the extent to which the initial state of geometry and orientation angles affect the device current. Experimental results confirm these effects.

Low-temperature Er3+ emission in Ge-S-Ga glasses excited by host absorption

The photoluminescence (PL) of a series of (GeS2)(80)(Ga2S3)(20) glasses doped with different amounts of Er (0.17, 0.35, 0.52, 1.05 and 1.39 at.%) at 77 and 4.2 K has been studied. The influence of the temperature on the emission cross-section of the PL bands at -> 1540, 980 and 820 nm under host excitation has been defined. A quenching effect of the host photoluminescence has been established from the compositional dependence of the PL intensity. It has been found that the present Er3+-doped Ge-S-Ga glasses posses PL lifetime values about 3.25 ms. (C) 2007 Elsevier B.V. All rights reserved.

How Effective Is The Data On Co-Occurrence Of Domains In Multi-Domain Proteins In Prediction Of Protein-Protein Interactions?

We explore the fuse of information on co-occurrence of domains in multi-domain proteins in predicting protein-protein interactions. The basic premise of our work is the assumption that domains co-occurring in a polypeptide chain undergo either structural or functional interactions among themselves. In this study we use a template dataset of domains in multidomain proteins and predict protein-protein interactions in a target organism. We note that maximum number of correct predictions of interacting protein domain families (158) is made in S. cerevisiae when the dataset of closely related organisms is used as the template followed by the more diverse dataset of bacterial proteins (48) and a dataset of randomly chosen proteins (23). We conclude that use of multi-domain information from organisms closely-related to the target can aid prediction of interacting protein families.

Enhanced Tetrahedral Ordering of Water Molecules in Minor Grooves of DNA: Relative Role of DNA Rigidity, Nanoconfinement, and Surface Specific Interactions

Confinement and Surface specific interactions call induce Structures otherwise unstable at that temperature and pressure. Here we Study the groove specific water dynamics ill the nucleic acid sequences, poly-AT and poly-GC, in long B-DNA duplex chains by large scale atomistic molecular dynamics simulations, accompanied by thermodynamic analysis. While water dynamics in the major groove remains insensitive to the sequence differences, exactly the opposite is true for the minor groove water. Much slower water dynamics observed in the minor grooves (especially in the AT minor) call be attributed to all enhanced tetrahedral ordering (< t(h)>) of water. The largest value of < t(h)> in the AT minor groove is related to the spine of hydration found in X-ray Structure. The calculated configurational entropy (S-C) of the water molecules is found to be correlated with the self-diffusion coefficient of water in different region via Adam-Gibbs relation D = A exp(-B/TSC), and also with < t(h)>.

Supramolecular Organization in Tetra Aqua (mu-8-Hydroxyquinoline-5-sulfonate) Barium (II) and Ag center dot center dot center dot I Interactions in a Pseudopolymorphic Form of (7-Iodo-8-hydroxyquinoline-5-sulfonate) Silver (I) Monohydrate

The complexes, Ba (HQS) (H2O)(4) (HQS = 8-hydroxyquinoline-5-sulfonic acid) (1) and Ag (HIQS) (H2O) (Ferron = 7-iodo-8-hydroxyquinoline-5-sulfonic acid) (2) have been synthesized and characterized by X-ray diffraction analysis and spectroscopic studies. In compound 1, Ba2+ ion has a nine-coordinate monocapped antiprismatic geometry. In compound 2, Ag+ has distorted tetrahedral coordination and Ag center dot center dot center dot I interactions generate the supramolecular architectures. The complexes have been characterized by FT-IR and UV-Visible measurements. In both the structures, the inversion-related organic ligands are stacked over one another leading to three-dimensional networks.

Host factor Ebp1 inhibits rinderpest virus transcription in vivo

ErbB3 binding protein Ebp1 has been shown to downregulate ErbB3 receptor-mediated signaling to inhibit cell proliferation. Rinderpest virus belongs to the family Paramyxoviridae and is characterized by the presence of a non-segmented negative-sense RNA genome. In this work, we show that rinderpest virus infection of Vero cells leads to the down-regulation of the host factor Ebp1, at both the mRNA and protein levels. Ebp1 protein has been shown to co-localize with viral inclusion bodies in infected cells, and it is packaged into virions, presumably through its interaction with the N protein or the N-RNA itself. Overexpression of Ebp1 inhibits viral transcription and multiplication in infected cells, suggesting that a mutual antagonism operates between host factor Ebp1 and the virus.

Exploring polymorphism by solvent mediation in potentially active herbicide Metribuzin: A subtle interplay of weak intermolecular interactions

Metribuzin, 4-amino-6-tert-butyl-3-methylthio- 1,2,4-triazin-5-one, exhibits polymorphic behaviour, crystallizing as plates and needles, driven by variation in solvent polarity, a delicate balance of weak intermolecular forces generating different molecular assemblies.

Peptide-lanthanide interactions. Crystal structure of a europium(III)-triglycine complex

Crystals of Eu-(Gly-Gly-Gly).(H2O)5.(ClO4)3 are triclinic, spacegroup P1BAR with a = 9.123 (2), b = 11.185 (5), c = 11.426 (2) angstrom; alpha = 90.79 (2), beta = 98.08 (1), gamma = 98.57 (2)-degrees; Z = 2. The europium cation is surrounded by four oxygens from three different peptide units and four oxygens from water molecules. The geometry around the metal is a distorted bi-capped trigonal prism. The peptide backbone conformation in this complex is compared with those in the free peptide and in various metal complexes. Considerable differences are observed between Eu(III) and Ca(II) complexes of triglycine. (C) Munksgaard 1994.

Interactions of linear dicationic molecules with lipid A: structural requisites for optimal binding affinity

The structural determinants of the binding affinity of linear dicationic molecules toward lipid A have been examined with respect to the distance between the terminal cationic functions, the basicity, and the type of cationic moieties using a series of spermidine derivatives and pentamidine analogs by fluorescence spectroscopic methods, The presence of two terminal cationic groups corresponds to enhanced affinity, A distinct sigmoidal relationship between the intercationic distance and affinity was observed with a sharp increase at 11 Angstrom, levelling off at about 13 Angstrom. The basicity (pK) and nature of the cationic functions are poor correlates of binding potency, since molecules bearing primary amino, imidazolino, or guanido termini are equipotent, The interaction of pentamidine, a bisamidine drug, with lipid A, characterized in considerable detail employing the putative intermolecular excimerization of the drug, suggests a stoichiometry of 1:1 in the resultant complex, The binding is driven almost exclusively by electrostatic forces, and is dependent on the ionization states of both lipid A and the drug, Under conditions when lipid A is highly disaggregated, pentamidine binds specifically to bis-phosphoryl- but not to monophosphoryl-lipid A indicating that both phosphate groups of lipid A are necessary for electrostatic interactions by the terminal amidininium groups of the drug, Based on these data, a structural model is proposed for the pentamidine-lipid A complex, which may be of value in designing endotoxin antagonists from first principles.