Synergy between the N-terminal and C-terminal domains of Mycobacterium tuberculosis HupB is essential for high-affinity binding, DNA supercoiling and inhibition of RecA-promoted strand exchange

The occurrence of DNA architectural proteins containing two functional domains derived from two different architectural proteins is an interesting emerging research theme in the field of nucleoid structure and function. Mycobacterium tuberculosis HupB, unlike Escherichia coli HU, is a two-domain protein that, in the N-terminal region, shows broad sequence homology with bacterial HU. The long C-terminal extension, on the other hand, contains seven PAKK/KAAK motifs, which are characteristic of the histone H1/H5 family of proteins. In this article, we describe several aspects of HupB function, in comparison with its truncated derivatives lacking either the C-terminus or N-terminus. We found that HupB binds a variety of DNA repair and replication intermediates with K(d) values in the nanomolar range. By contrast, the N-terminal fragment of M. tuberculosis HupB (HupB(MtbN)) showed diminished DNA-binding activity, with K(d) values in the micromolar range, and the C-terminal domain was completely devoid of DNA-binding activity. Unlike HupB(MtbN), HupB was able to constrain DNA in negative supercoils and introduce negative superhelical turns into relaxed DNA. Similarly, HupB exerted a robust inhibitory effect on DNA strand exchange promoted by cognate and noncognate RecA proteins, whereas HupB(MtbN), even at a 50-fold molar excess, had no inhibitory effect. Considered together, these results suggest that synergy between the N-terminal and C-terminal domains of HupB is essential for its DNA-binding ability, and to modulate the topological features of DNA, which has implications for processes such as DNA compaction, gene regulation, homologous recombination, and DNA repair.

Structure and Bonding in Stannadiphospholes and their Dianions SnC(2)P(2)R(2)(m) (R=H, tBu m=0,-2): A Comparative Study with C(5)H(5)(+) and C(5)H(5)(-) Analogues

The potential energy surfaces of both neutral and dianionic SnC(2)P(2)R(2) (R=H, tBu) ring systems have been explored at the B3PW91/LANL2DZ (Sn) and 6-311 + G* (other atoms) level. In the neutral isomers the global minimum is a nido structure in which a 1,2-diphosphocyclobutadiene ring (1,2-DPCB) is capped by the Sn. Interestingly, the structure established by Xray diffraction analysis, for R=tBu, is a 1,3-DPCB ring capped by Sn and it is 2.4 kcal mol(-1) higher in energy than the 1,2-DPCB ring isomer. This is possibly related to the kinetic stability of the 1,3-DPCB ring, which might originate from the synthetic precursor ZrCp(2)tBu(2)C(2)P(2). In the case of the dianionic isomers we observe only a 6 pi-electron aromatic structure as the global minimum, similarly to the cases of our previously reported results with other types of heterodiphospholes.([1,4,19]) The existence of large numbers of cluster-type isomers in neutral and 6 pi-planar structures in the dianions SnC(2)P(2)R(2)(2-) (R=H, tBu) is due to 3D aromaticity in neutral clusters and to 2D pi aromaticity of the dianionic rings. Relative energies of positional isomers mainly depend on: 1) the valency and coordination number of the Sn centre, 2) individual bond strengths, and 3) the steric effect of tBu groups. A comparison of neutral stannadiphospholes with other structurally related C(5)H(5)(+) analogues indicates that Sn might be a better isolobal analogue to P(+) than to BH or CH(+). The variation in global minima in these C(5)H(5)(+) analogues is due to characteristic features such as 1) the different valencies of C, B, P and Sn, 2) the electron deficiency of B, 3) weaker p pi-p pi bonding by P and Sn atoms, and 4) the tendency of electropositive elements to donate electrons to nido clusters. Unlike the C5H5+ systems, all C(5)H(5)(-) analogues have 6 pi-planar aromatic structures as global minima. The differences in the relative ordering of the positional isomers and ligating properties are significant and depend on 1) the nature of the pi orbitals involved, and 2) effective overlap of orbitals.

Coordination-Driven Self-Assembly of 2D-Metallamacrocycles Using a New Carbazole-Based Dipyridyl Donor: Synthesis, Characterization, and C-60 Binding Study

A new carbazole-based 90 degrees dipyridyl donor 3,6-di(4-pyridylethynyl)carbazole (L) containing carbazole-ethynyl functionality is synthesized in reasonable yield using the Sonagashira coupling reaction. Multinuclear NMR, electrospray ionization-mass spectrometry (ESI-MS), including single crystal X-ray diffraction analysis characterized this 90 degrees building unit. The stoichiometry combination of L with several Pd(II)/Pt(II)-based 90 degrees acceptors (1a-1d) yielded 2 + 2] self-assembled metallacycles (2a-2d) under mild conditions in quantitative yields 1a = cis-(dppf)Pd(OTf)(2); 1b = cis-(dppf)Pt(OTf)(2); 1c = cis-(tmen)Pd(NO3)(2); 1d = 3,6-bis{trans-Pt(C C) (PEt3)(2)(NO3))carbazole]. All these macrocycles were characterized by various spectroscopic techniques, and the molecular structure of 2a was unambiguously determined by single crystal X-ray diffraction analysis. Incorporation of ethynyl functionality to the carbazole backbone causes the resulted macrocycles (2a-2d) to be pi-electron rich and thereby exhibit strong emission characteristics. The macrocycle 2a has a large internal concave aromatic surface. The fluorescence quenching study suggests that 2a forms a similar to 1:1 complex with C-60 with a high association constant of K-sv = 1.0 X 10(5) M-1.

Structural characterization and molecular order of rodlike mesogens with three- and four-ring core by XRD and C-13 NMR spectroscopy

Structural characterizations using XRD and C-13 NMR spectroscopy of two rodlike mesogens consisting of (i) three phenyl ring core with a polar cyano terminal and (ii) four phenyl ring core with flexible dodecyl terminal chain are presented. The three-ring-core mesogen with cyano terminal exhibits enantiotropic smectic A phase while the four-ring mesogen reveals polymesomorphism and shows enantiotropic nematic, smectic C, and tilted hexatic phases. The molecular organization in the three-ring mesogen is found to be partial bilayer smectic Ad type, and the interdigitation of the molecules in the neighboring layers is attributed to the presence of the polar terminal group. For the four-ring mesogen, the XRD results confirm the existence of the smectic C and the tilted hexatic mesophases. A thermal variation of the layer spacing across the smectic C phase followed by a discrete jump at the transition to the tilted hexatic phase is also observed. The tilt angles have been estimated to be about 45 degrees in the smectic C phase and about 40 degrees in tilted hexatic phase. C-13 NMR results indicate that in the mesophase the molecules are aligned parallel to the magnetic field. From the C-13-H-1 dipolar couplings determined from the 2D experiments, the overall order parameter for the three-ring mesogen in its smectic A phase has been estimated to be 0.72 while values ranging from 0.88 to 0.44 have been obtained for the four-ring mesogen as it passes from the tilted hexatic to the nematic phase. The orientations of the different rings of the core unit with respect to each other and also with respect to the long axis of the molecule have also been obtained.

Dense network of O-H ... O and C-H ... O interactions in the solid state structure of n-pentyl-2-chloro-2-deoxy-alpha-D-manno-sept 3-uloside

Single crystal X-ray structural analysis of a septanoside, namely, n-pentyl-2-chloro-2-deoxy sept-3-uloside (1) provides many finer details of the molecular structure, in addition to its preferred twist-chair conformation, namely, (TC3,4)-T-5,6 conformation. Structural analysis reveals a dense network of O-H...O, C-H...O and van der Waals interactions that stabilize interdigitized, planar bi-layer structure of the crystal lattice. (C) 2014 Elsevier Ltd. All rights reserved.

Effect of adsorbate loading on selectivity during adsorption of C/C and C/C n-alkane binary mixtures in silicalite

Adsorption experiments of mixtures of long chain alkanes into silicalite under liquid phase conditions show selectivity inversion and azeotrope formation. These effects are due to the subtle interplay between the size of the adsorbed molecules and pore topology of the adsorbent. In this study, the selective uptake of lighter component during liquid phase adsorption of C/C and C/C n-alkane binary mixtures in the zeolite silicalite is understood through configurational bias grand-canonical Monte Carlo molecular simulation technique and a coarse-grained siting analysis. The simulations are conducted under conditions of low and intermediate levels of loading. The siting pattern of the adsorbates inside the zeolite pores explain the selectivity as seen in experiments.

On the Utility of Microscopy and C-Scan Techniques in the Study of Defects Arising From Resin Infusion Process and a Study on the Influence of Voids on the Impact Behavior of CFRP Composites

Carbon Fiber Reinforced Plastic composites were fabricated through vacuum resin infusion technology by adopting two different processing conditions, viz., vacuum only in the first and vacuum plus external pressure in the next, in order to generate two levels of void-bearing samples. They were relatively graded as higher and lower void-bearing ones, respectively. Microscopy and C-scan techniques were utilized to describe the presence of voids arising from the two different processing parameters. Further, to determine the influence of voids on impact behavior, the fabricated +45 degrees/90 degrees/-45 degrees composite samples were subjected to low velocity impacts. The tests show impact properties like peak load and energy to peak load registering higher values for the lower void-bearing case where as the total energy, energy for propagation and ductility indexes were higher for the higher void-bearing ones. Fractographic analysis showed that higher void-bearing samples display lower number of separation of layers in the laminate. These and other results are described and discussed in this report.

Insights into the Functional Roles of N-Terminal and C-Terminal Domains of Helicobacter pylori DprA

DNA processing protein A (DprA) plays a crucial role in the process of natural transformation. This is accomplished through binding and subsequent protection of incoming foreign DNA during the process of internalization. DprA along with Single stranded DNA binding protein A (SsbA) acts as an accessory factor for RecA mediated DNA strand exchange. H. pylori DprA (HpDprA) is divided into an N-terminal domain and a C-terminal domain. In the present study, individual domains of HpDprA have been characterized for their ability to bind single stranded (ssDNA) and double stranded DNA (dsDNA). Oligomeric studies revealed that HpDprA possesses two sites for dimerization which enables HpDprA to form large and tightly packed complexes with ss and dsDNA. While the N-terminal domain was found to be sufficient for binding with ss or ds DNA, C-terminal domain has an important role in the assembly of poly-nucleoprotein complex. Using site directed mutagenesis approach, we show that a pocket comprising positively charged amino acids in the N-terminal domain has an important role in the binding of ss and dsDNA. Together, a functional cross talk between the two domains of HpDprA facilitating the binding and formation of higher order complex with DNA is discussed.

Contrasting Electronic Requirements for C-H Binding and C-H Activation in d(6) Half-Sandwich Complexes of Rhenium and Tungsten

A computational study of the interaction half-sandwich metal fragments (metal=Re/W, electron count=d(6)), containing linear nitrosyl (NO+), carbon monoxide (CO), trifluorophosphine (PF3), N-heterocyclic carbene (NHC) ligands with alkanes are conducted using density functional theory employing the hybrid meta-GGA functional (M06). Electron deficiency on the metal increases with the ligand in the order NHC < CO < PF3 < NO+. Electron-withdrawing ligands like NO+ lead to more stable alkane complexes than NHC, a strong electron donor. Energy decomposition analysis shows that stabilization is due to orbital interaction involving charge transfer from the alkane to the metal. Reactivity and dynamics of the alkane fragment are facilitated by electron donors on the metal. These results match most of the experimental results known for CO and PF3 complexes. The study suggests activation of alkane in metal complexes to be facile with strong donor ligands like NHC. (C) 2015 Wiley Periodicals, Inc.

Mono layer to Interdigitated Partial Bilayer Smectic C Transition in Thiophene-Based Spacer Mesogens: X-ray Diffraction and C-13 Nuclear Magnetic Resonance Studies

Mesophase organization of molecules built with thiophene at the center and linked via flexible spacers to rigid side arm core units and terminal alkoxy chains has been investigated. Thirty homologues realized by varying the span of the spacers as well as the length of the terminal chains have been studied. In addition to the enantiotropic nematic phase observed for all the mesogens, the increase of the spacer as well as the terminal chain lengths resulted in the smectic C phase. The molecular organization in the smectic phase as investigated by temperature dependent X-ray diffraction measurements revealed an interesting behavior that depended on the length of the spacer vis-a-vis the length of the terminal chain. Thus, a tilted interdigitated partial bilayer organization was observed for molecules with a shorter spacer length, while a tilted monolayer arrangement was observed for those with a longer spacer length. High-resolution solid state C-13 NMR studies carried out for representative mesogens indicated a U-shape for all the molecules, indicating that intermolecular interactions and molecular dynamics rather than molecular shape are responsible for the observed behavior. Models for the mesophase organization have been considered and the results understood in terms of segregation of incompatible parts of the mesogens combined with steric frustration leading to the observed lamellar order.

Functional roles of N-terminal and C-terminal domains in the overall activity of a novel single-stranded DNA binding protein of Deinococcus radiodurans

Single-stranded DNA binding protein (Ssb) of Deinococcus radiodurans comprises N- and C-terminal oligonucleotide/oligosaccharide binding (OB) folds connected by a beta hairpin connector. To assign functional roles to the individual OB folds, we generated three Ssb variants: Ssb(N) (N-terminal without connector), Ssb(NC) (N-terminal with connector) and Ssb(C) (C-terminal), each harboring one OB fold. Both Ssb(N) and Ssb(NC) displayed weak single-stranded DNA (ssDNA) binding activity, compared to the full-length Ssb (Ssb(FL)). The level of ssDNA binding activity displayed by SsbC was intermediate between Ssb(FL) and Ssb(N). Ssb(C) and Ssb(FL) predominantly existed as homo-dimers while Ssb(NC)/Ssb(N) formed different oligomeric forms. In vitro, Ssb(NC) or Ssb(N) formed a binary complex with Ssb(C) that displayed enhanced ssDNA binding activity. Unlike Ssb(FL), Ssb variants were able to differentially modulate topoisomerase-I activity, but failed to stimulate Deinococcal RecA-promoted DNA strand exchange. The results suggest that the C-terminal OB fold is primarily responsible for ssDNA binding. The N-terminal OB fold binds weakly to ssDNA but is involved in multimerization. (C) 2015 The Authors. Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies. This is an open access article under the CC BY-NC-ND license.

The pottery from A and C-Group tombs at Serra West in the Museum of Natural History, La Plata

Abstract: The Museum of Natural History, La Plata, Argentina, houses a ceramic collection of the A-Group and C-Group cultures from Nubian tombs at Serra West (AA and ACS cemeteries), on the west bank of the Nile in Lower Nubia. It has been originated from the division after the excavations made by the Franco-Argentine Archaeological Expedition in Sudan between 1961 and 1963, as part of the UNESCO campaigns to save the Nubian monuments.

Synopsis of biological data on the porgies, Calamus arctifrons and C. proridens (Pisces: Sparidae)

Information on the biology and fishery resources of two common species of western Atlantic porgies, Calamus areli/rons and C. proridens, is compiled, reviewed, and analyzed in the FAO species synopsis style. (PDF file contains 25 pages.)

Investigation of nematode Eustrongylides larvae infections in mudfish Clarias gariepinus and C. anguillaris from Bida floodplain of Nigeria

This is the first report and record of the determination whether mudfish Clarias were infected with the larvae of the nematode Eustrongylides. Also, documented the assessment of the socio-economic perceptions of three groups of fisher folks on the economy of infected mudfish Clarias fishing activities. Fifty-six (67.5%) of 83 mudfish Clarias caught by artisanal fisher folks were examined for the presence of the larvae of the nematode Eustrongylides. All the 8 sampled fishing localities in Bida floodplain of Nigeria had a mean intensity and abundance of at least 3 and 1 worm per fish per site, respectively. Two hundred and one (96.2%) of 209 worms recovered were from the musculatures at different depths resulting in undulations on the skin surfaces as grub-like presentations. The three groups of fisher folks assessed encountered economic losses from nematode infected mudfish Clarias which attract much debates or rejections during marketing due to its aesthetically displeasing appearance, faster deterioration, higher fragility in smoked form coupled with poorer taste compared to the wholesome ones. Infected female mudfish Clarias had higher worm burden than the males, for each fishing locality