The Non-catalytic ``Cap Domain'' of a Mycobacterial Metallophosphoesterase Regulates Its Expression and Localization in the Cell

Despite highly conserved core catalytic domains, members of the metallophosphoesterase (MPE) superfamily perform diverse and crucial functions ranging from nucleotide and nucleic acid metabolism to phospholipid hydrolysis. Unique structural elements outside of the catalytic core called ``cap domains'' are thought to provide specialization to these enzymes; however, no directed study has been performed to substantiate this. The cap domain of Rv0805, an MPE from Mycobacterium tuberculosis, is located C-terminal to its catalytic domain and is dispensable for the catalytic activity of this enzyme in vitro. We show here that this C-terminal extension (CTE) mediates in vivo localization of the protein to the cell membrane and cell wall as well as modulates expression levels of Rv0805 in mycobacteria. We also demonstrate that Rv0805 interacts with the cell wall of mycobacteria, possibly with the mycolyl-arabinogalactan-peptidoglycan complex, by virtue of its C terminus, a hitherto unknown property of this MPE. Using a panel of mutant proteins, we identify interactions between active site residues of Rv0805 and the CTE that determine its association with the cell wall. Finally, we show that Rv0805 and a truncated mutant devoid of the CTE produce different phenotypic effects when expressed in mycobacteria. Our study thus provides a detailed dissection of the functions of the cap domain of an MPE and suggests that the repertoire of cellular functions of MPEs cannot be understood without exploring the modulatory effects of these subdomains.

Stable isotope evidence for ca. 2.7-Ga-old Archean cap carbonates from the Dharwar Supergroup, southern India

Carbon isotope compositions of carbonate rocks from similar to 2.7-Ga-old Neoarchean Vanivilas Formation of the Dharwar Supergroup presented earlier by us are re-evaluated in this study, besides oxygen isotope compositions of a few silica dolomite pairs. The purpose of such a revisit assumes significance in view of recent field evidences that suggest a glaciomarine origin for the matrix-supported conglomerate member, the Talya conglomerate, which underlies the carbonate rocks of the Vanivilas Formation. An in-depth analysis of carbon isotope data reveals preservation of their pristine character despite the rocks having been subjected to metamorphism to different degrees (from lower greenschist to lower amphibolite facies). The dolomitic member of Vanivilas Formation of Marikanive area is characterized by highly depleted delta C-13 value (up to -5 parts per thousand VPDB) and merits as the Indian example of ca. 2.7-Ga-old cap carbonate. This inference is further supported by estimated low temperature of equilibration documented by a few silica dolomite pairs from the Vanivilas Formation collected near Kalche area. These pairs show evidence for oxygen isotopic equilibrium at low temperatures (similar to 0-20 degrees C) with depleted water (delta O-18 = -21 parts per thousand to -15 parts per thousand VSMOW) of glacial origin. We propose that the mineral pairs were deposited during the deglaciation period when the ocean temperature was in its gradual restoration phase. The dolomite of Marikanive area is the first record of cap carbonates from the Indian subcontinent with Neoarchean antiquity.

p53 and little brother p53/47: linking IRES activities with protein functions

The tumor suppressor p53 represents a paradigm for gene regulation. Its rapid induction in response to DNA damage conditions has been attributed to both increased half-life of p53 protein and also increased translation of p53 mRNA. Recent advances in our understanding of the post-transcriptional regulation of p53 include the discovery of internal ribosome entry sites (IRESs) within the p53 mRNA. These IRES elements regulate the translation of the full length as well as the N-terminally truncated isoform, p53/47. The p53/47 isoform is generated by alternative initiation at an internal AUG codon present within the p53 ORF. The aim of this review is to summarize the role of translational control mechanisms in regulating p53 functions. We discuss here in detail how diverse cellular stress pathways trigger alterations in the cap-dependent and cap-independent translation of p53 mRNA and how changes in the relative expression levels of p53 isoforms result in more differentiated p53 activity.

Pentoxifylline induces hyperactivation and acrosome reaction in spermatozoa of golden hamsters: changes in motility kinematics

Pentoxifylline (PF) is used to enhance motility of spermatozoa from infertile human subjects. We have previously shown that 0.45 mM PF improved capacitation of spermatozoa and fertilization of oocytes in vitro in hamsters. The present study was carried out to assess PF- induced changes in motility kinematics of hamster spermatozoa by a computer-aided sperm analyser (CASA) and determine the timing of onset of hyperactivation (HA) and acrosome reaction (AR) in PF-treated spermatozoa. Motility kinematics were analysed by CASA for 0-8 h in the absence or presence of 0.45 mM PF in Tyrode's medium supplemented with lactate, pyruvate and polyvinyl alcohol (TLP-PVA) or in TLP-PVA with bovine serum albumin (TALP-PVA). Conventional assessment was also made on the percentage of motility and quality of motility of spermatozoa; values were expressed as sperm motility index (SMI). Both in TALP-PVA and TLP-PVA, PF markedly increased SMI, especially the quality of motility (P < 0.02) by 2-3 h which was sustained up to 6 h. The motility kinematic data of PF-treated spermatozoa in TALP-PVA showed that average path velocity, curvilinear velocity and amplitude of lateral head displacement significantly (P < 0.05) increased as early as 2 h, with the expected decrease in straightness (STR) and linearity (LIN). Similar changes were also observed with PF-treated spermatozoa in TLP-PVA. Moreover, the percentage of hyperactivated spermatozoa in PF-treated samples was significantly (P < 0.001) higher than the untreated control at 2 h. To determine whether PF could induce AR, independent of bovine serum albumin, quantitative AR was assessed by observing the presence or absence of acrosomal cap on viable spermatozoa. PF significantly (P < 0.001) increased the percentage of AR as early as 2 h, reaching maximum at 4 h both in TALP-PVA (P < 0.05) and in TLP-PVA (P < 0.001). These results show that, in hamsters, PF induces early onset (by 2 h) of HA and AR and increases the proportion of spermatozoa undergoing physiological maturation.

Stuffed fullerenelike boron carbide nanoclusters

Viable stuffed fullerenelike boron carbide nanoclusters, C50B34, C48B36-2, and their isomers based on an icosahedral B-84 fragment of elemental beta-rhombohedral boron have been investigated using density functional theory calculations. The structure and the stability of these clusters are rationalized using the polyhedral skeletal electron counting and ring-cap orbital overlap compatibility rules. The curvature of the fullerene was found to play a vital role in achieving the most stable isomer C50B34(3B). The large highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gaps, three dimensional aromaticity, and electron detachment energies support their high stability. Further, the IR and Raman active modes were recognized.

Real Theta Characteristics And Automorphisms Of A Real Curve

Let X be a geometrically irreductble smooth projective cruve defined over R. of genus at least 2. that admits a nontrivial automorphism, sigma. Assume that X does not have any real points. Let tau be the antiholomorphic involution of the complexification lambda(C) of X. We show that if the action of sigma on the set S(X) of all real theta characteristics of X is trivial. then the order of sigma is even, say 2k and the automorphism tau o (sigma) over cap (lambda) of X-C has a fixed point, where (sigma) over cap is the automorphism of X x C-R defined by sigma We then show that there exists X with a real point and admitting a nontrivial automorphism sigma, such that the action of sigma on S(X) is trivial, while X/ not equal P-R(1) We also give an example of X with no real points and admitting a nontrivial automorphisim sigma such that the automorphism tau o (sigma) over cap (lambda) has a fixed point, the action of sigma on S(X) is trivial, and X/ not equal P-R(1)

Disulfide conformation and design at helix N-termini

To understand structural and thermodynamic features of disulfides within an alpha-helix, a non-redundant dataset comprising of 5025 polypeptide chains containing 2311 disulfides was examined. Thirty-five examples were found of intrahelical disulfides involving a CXXC motif between the N-Cap and third helical positions. GLY and PRO were the most common amino acids at positions 1 and 2, respectively. The N-Cap residue for disulfide bonded CXXC motifs had average values of (-112 +/- 25.2 degrees, 106 +/- 25.4 degrees). To further explore conformational requirements for intrahelical disulfides, CYS pairs were introduced at positions N-Cap-3; 1,4; 7,10 in two helices of an Escherichia coli thioredoxin mutant lacking its active site disulfide (nSS Trx). In both helices, disulfides formed spontaneously during purification only at positions N-Cap-3. Mutant stabilities were characterized by chemical denaturation studies (in both oxidized and reduced states) and differential scanning calorimetry (oxidized state only). All oxidized as well as reduced mutants were destabilized relative to nSS Trx. All mutants were redox active, but showed decreased activity relative to wild-type thioredoxin. Such engineered disulfides can be used to probe helix start sites in proteins of unknown structure and to introduce redox activity into proteins. Conversely, a protein with CYS residues at positions N-Cap and 3 of an alpha-helix is likely to have redox activity.

Conformational characteristics of asparaginyl residues in proteins

Backbone conformations at 1064 asparaginyl residues in 123 non-homologous, high-resolution X-ray structures of proteins were analysed. Asn adopts conformations in left-handed x-helical region and other partially allowed regions in the Ramachandran map more readily than any other non-glycyl residue. Asn conformational clusters in the (phi,psi) regions of left-handed alpha-helix, right-handed alpha-helix and extended (beta) strands were investigated in detail for their occurrence in various secondary structures, especially in beta-turn regions. Preferences were observed for Asn conformations in different positions in various beta-turn types, including the first and fourth positions of the turn. Asparaginyl residues with extended conformations are found to occur frequently in irregular regions, although they are expected to occur predominantly in extended strands or in the third position of type II beta-turns. Asn conformations at the N-cap positions of helices strongly prefer extended conformation than alpha(L), which seems to be characteristic of non-glycyl residues at that position. In the linkers connecting two extended strands and those connecting an alpha-helix and an extended strand, Asn with alpha(L) or alpha(R) conformation is more favoured than Asn with the beta-conformation. Analysis of Asn-Asn doublets and Asn-X-Asn triplets permitted identification of conformational families in such sequences. Results of this investigation provide useful hints in modelling Asn-rich regions in proteins such as malaria parasite coat protein. (C) Munksgaard 1994.

Faster Algorithms for All-pairs Approximate Shortest Paths in Undirected Graphs

Let G - (V, E) be a weighted undirected graph having nonnegative edge weights. An estimate (delta) over cap (u, v) of the actual distance d( u, v) between u, v is an element of V is said to be of stretch t if and only if delta(u, v) <= (delta) over cap (u, v) <= t . delta(u, v). Computing all-pairs small stretch distances efficiently ( both in terms of time and space) is a well-studied problem in graph algorithms. We present a simple, novel, and generic scheme for all-pairs approximate shortest paths. Using this scheme and some new ideas and tools, we design faster algorithms for all-pairs t-stretch distances for a whole range of stretch t, and we also answer an open question posed by Thorup and Zwick in their seminal paper [J. ACM, 52 (2005), pp. 1-24].

Heterogeneous nucleation of solidification of cadmium particles embedded in an aluminium matrix

A hypomonotectic alloy of Al-4.5wt%Cd has been manufactured by melt spinning and the resulting microstructure examined by transmission electron microscopy. As-melt spun hypomonotectic Al-4.5wt%Cd consists of a homogeneous distribution of faceted 5 to 120 nm diameter cadmium particles embedded in a matrix of aluminium, formed during the monotectic solidification reaction. The cadmium particles exhibit an orientation relationship with the aluminium matrix of {111}Al//{0001}Cd and lang110rangAlAl//lang11¯20> Cd, with four cadmium particle variants depending upon which of the four {111}Al planes is parallel to {0001}Cd. The cadmium particles exibit a distorted cuboctahedral shape, bounded by six curved {100}Al//{20¯23}Cd facets, six curved {111}Al/{40¯43}Cd facets and two flat {111}Al//{0001}Cd facets. The as-melt spun cadmium particle shape is metastable and the cadmium particles equilibrate during heat treatment below the cadmium melting point, becoming elongated to increase the surface area and decrease the separation of the {111}Al//{0001}Cd facets. The equilibrium cadmium particle shape and, therefore, the anisotropy of solid aluminium-solid cadmium and solid aluminium -liquid cadmium surface energies have been monitored by in situ heating in the transmission electron microscope over the temperature range between room temperature and 420 °C. The anisotropy of solid aluminium-solid cadmium surface energy is constant between room temperature and the cadmium melting point, with the {100}Al//{20¯23}Cd surface energy on average 40% greater than the {111}Al//{0001}Cd surface energy, and 10% greater than the {111}Al//{40¯43Cd surface energy. When the cadmium particles melt at temperatures above 321 °C, the {100}Al//{20¯23}Cd facets disappear and the {111}Al//{40¯43}Cd and {111}A1//{0001}Cd surface energies become equal. The {111}Al facets do not disappear when the cadmium particles melt, and the anisotropy of solid aluminium-liquid cadmium surface energy decreases gradually with increasing temperature above the cadmium melting point. The kinetics of cadmium solidification have been examined by heating and cooling experiments in a differential scanning calorimeter over a range of heating and cooling rates. Cadmium particle solidification is nucleated catalytically by the surrounding aluminium matrix on the {111}Al faceted surfaces, with an undercooling of 56 K and a contact angle of 42 °. The nucleation kinetics of cadmium particle solidification are in good agreement with the hemispherical cap model of heterogeneous nucleation.

Dielectric relaxation in bismuth layer-structured BaBi4Ti4O15 ferroelectric ceramics

The dielectric properties of BaBi4Ti4O15 ceramics were investigated as a function of frequency (10(2)-10(6) Hz) at various temperatures (30 degrees C-470 degrees C), covering the phase transition temperature. Two different conduction mechanisms were obtained by fitting the complex impedance data to Cole-Cole equation. The grain and grain boundary resistivities were found to follow the Arrhenius law associated with activation energies: E-g similar to 1.12 eV below T-m and E-g similar to 0.70 eV above T-m for the grain conduction; and E-gb similar to 0.93 eV below T-m and E-gb similar to 0.71 eV above T-m for the grain boundary conduction. Relaxation times extracted using imaginary part of complex impedance Z `'(omega) and modulus M `'(omega) were also found to follow the Arrhenius law and showed an anomaly around the phase transition temperature. The frequency dependence of conductivity was interpreted in terms of the jump relaxation model and was fitted to the double power law. (C) 2010 Elsevier B. V. All rights reserved.

Self-assembled composite nano-materials exploiting a thermo reversible n-acene fibrillar scaffold and organic-capped ZnO nanoparticles

An organic-inorganic composite material is obtained by self-assembly of 2,3-didecyloxy-anthracene (DDOA), an organogelator of butanol, and organic-capped ZnO nanoparticles (NPs). The ligand 3, 2,3-di(6-oxy-n-hexanoic acid)-anthracene, designed to cap ZnO and interact with the DDOA nanofibers by structural similarity, improves the dispersion of the NPs into the organogel. The composite material displays mechanical properties similar to those of the pristine DDOA organogel, but gelates at a lower critical concentration and emits significantly less, even in the presence of very small amounts of ZnO NPs. The ligand 3 could also act as a relay to promote the photo-induced quenching process.

The Reaction of a Nitro-Capped Cobalt(III) Cage Complex With Base: the Crystal Structure of a Contracted Cage Complex, and the Mechanism of Its Formation

The synthesis, properties and crystal structure of the cage complex (1-hydroxy-8-methyl-3,6,10,13,15,18-hexaazabicyclo[6.6.5]nonadecane)cobalt(III) chloride hydrate ([Co(Me,OH-absar)] C13.H2O) are reported. The mechanism of the formation of this contracted cavity cage from a nitro-capped hexaazabicycloicosane type cage has been investigated. Treatment of (1-methyl-8-nitro-3,6,10,13,16,19-hexaazabicyclo[6.6.6]icosane)cobalt(III) chloride ([Co(Me,NO2-sar)] 3+) with excess base in aqueous solution leads initially to rapid (t1/2 < 1 ms) and reversible deprotonation of one coordinated secondary amine. This species undergoes a retro-Mannich type reaction and imine hydrolysis (t1/2 almost-equal-to 90 s). Quenching the reaction with acid gives rise to a pair of isomeric intermediate species which have been isolated and characterized. They have a pendant arm macrocyclic structure, resulting from the loss of a methylene unit from one of the arms of the cap. Heating either isomer in aqueous solution gives the new cage compound with the contracted cap. It is postulated that this occurs through a Nef reaction, resulting in the formation of a ketone which then condenses with the coordinated primary amine. A comparison with the corresponding bicycloicosane analogue indicates a reduced chromophoric cavity size for the contracted cage. The reduction potential of the cobalt(III)/cobalt(II) couple is 170 mV more negative for the smaller cage, and, in the electronic spectrum of the cobalt(III) complex, the d-d transitions are both shifted to higher energy, corresponding to a stronger ligand field.

An experimental investigation into pile group-layered soil interaction

An interaction analysis of an axially loaded single pile and pile group with and without a pile cap in a layered soil medium has been investigated using the two-dimensional photoelastic method. A study of the pile or pile group behaviour has been made, varying the pile cap thickness as well as the embedded length of the pile in the hard stratum. The shear stress distribution along the pile-soil interface, non-dimensionalized settlement values of the single pile and the interaction factor for the pile group have been presented. Wherever possible, the results of the present analysis have been compared with available numerical solutions.