Photolabeling of the EcoP15 DNA methyltransferase with S-adenosyl-l-methionine

Radioactivity from S-adenosyl-L-[methyl-H-3] methionine ([methyl-H-3]AdoMet) was bound to the EcoP15 DNA methyltransferase (M.EcoP15) following short-wave ultraviolet (UV) irradiation. The labeled protein was subjected to polyacrylamide-gel electrophoresis in the presence of sodium dodecyl sulfate (SDS-PAGE), and detected by fluorography and autoradiography. Labeling was found to be dependent on the concentration of AdoMet and time of UV irradiation. The photolabeling by [methyl-H-3]AdoMet was specific and blocked by S-adenosyl-L-homocysteine (AdoHcy) and sinefungin which are known to function as competitive inhibitors. Limited digestion of the M EcoP15-AdoMet adduct by Staphylococcus aureus protease V8 generated three peptides of approx. 50, 32 and 30 kDa; Interestingly, only the 30-kDa peptide fragment contained radioactivity, as detected by SDS-PAGE, followed by fluorography and autoradiography. Further, sequencing of a few amino acids at the N-terminus of these peptides showed that the 30-kDa fragment was the N-terminal portion of M.EcoP15, These results suggest that photolabeling is at the AdoMet-binding site and that the N-terminal half of M.EcoP15 may be involved in substrate binding.

Calcium/Calmodulin Dependent Protein Kinase II Bound to NMDA Receptor 2B Subunit Exhibits Increased ATP Affinity and Attenuated Dephosphorylation

Calcium/calmodulin dependent protein kinase II (CaMKII) is implicated to play a key role in learning and memory. NR2B subunit of N-methyl-D-aspartate receptor (NMDAR) is a high affinity binding partner of CaMKII at the postsynaptic membrane. NR2B binds to the T-site of CaMKII and modulates its catalysis. By direct measurement using isothermal titration calorimetry (ITC), we show that NR2B binding causes about 11 fold increase in the affinity of CaMKII for ATP gamma S, an analogue of ATP. ITC data is also consistent with an ordered binding mechanism for CaMKII with ATP binding the catalytic site first followed by peptide substrate. We also show that dephosphorylation of phospho-Thr(286)-alpha-CaMKII is attenuated when NR2B is bound to CaMKII. This favors the persistence of Thr(286) autophosphorylated state of CaMKII in a CaMKII/phosphatase conjugate system in vitro. Overall our data indicate that the NR2B- bound state of CaMKII attains unique biochemical properties which could help in the efficient functioning of the proposed molecular switch supporting synaptic memory.

Constructions of 2D-Metallamacrocycles Using Half-Sandwich Ru-2(II) Precursors: Synthesis, Molecular Structures, and Self-Selection for a Single Linkage Isomer

Coordination-driven self-assembly of oxalato-bridged half-sandwich p-cymene ruthenium complex Ru-2(mu-eta(4)-C2O4)(MeOH)(2)(eta(6)-p-cymene)(2)] (O3SCF3)(2) (1a) with several ditopic donors (L-a-L-d) in methanol affords a series of bi- and tetranuclear metallamacrocycles (2a and 3-5). Similarly, the combination of 2,5-dihydroxy-1,4-benzoquinonato (dhbq)-bridged binuclear complex Ru-2(mu-eta(4)-C6H2O4)(MeOH)(2)(eta(6)-p-cymene)(2)](O3SCF3)(2) (1b) with a flexible bidentate amide linker (L-a) in 1:1 molar ratio gave the corresponding tetranuclear complex 2b. All the macrocycles were isolated as their triflate salts in high yields and were fully characterized by various spectroscopic techniques. Finally, the molecular structures of all the assemblies were determined unambiguously by single-crystal X-diffraction analysis. Interestingly, the combination of acceptor 1a or 1b with an unsymmetrical linear ditopic donor L-a results in a self-sorted linkage isomeric (head-to-tail) macrocycle (2a or 2b) despite the possibility of formation of two different isomeric macrocycles (head-to-head or head-to-tail) due to different connectivity of the donor. Molecular structures of the complexes 2a and 2b showed tetranuclear rectangular geometry with dimensions of 5.51 angstrom x 13.29 angstrom for 2a and 7.91 angstrom x 13.46 angstrom for 2b. In both cases, two binuclear Ru-2(II) building blocks are connected by a mu-N-(4-pyridyl)isonicotinamide donor in a head-to-tail fashion. Surprisingly, the macrocycle 2a loses one counteranion and cocrystallizes with monodeprotonated 1,3,5-trihydroxybenzene via strong intermolecular pi-pi stacking and hydrogen bonding. The tweezer complex 3 showed strong fluorescence in solution, and it showed fluorescence sensing toward nitroaromatic compounds. A fluorescence study demonstrated a marked quenching of the initial fluorescence intensity of the macrocycle 3 upon gradual addition of trinitrotoluene and exhibits significant fluorescence quenching response only for nitroaromatic compounds compared to various other aromatic compounds tested.

Reentrant insulator-metal transition in the half-filled Hubbard model

Using the d=infinity or local-approximation approach to the half-filled Hubbard model on a compressible lattice, we present a detailed study of the transport and structural properties near the paramagnetic metal-insulator transition. The results describe qualitatively most of the observed data in V2O3, including the metal-insulator-metal crossover [Kuwamoto et al., Phys. Rev. B 22, 2626 (1980)]. In addition, we discuss an interesting and intrinsic reentrance feature in the resistivity of the half-filled Hubbard model at high temperatures.

A polynomial bound on the number of light cycles in an undirected graph

Let G be an undirected graph with a positive real weight on each edge. It is shown that the number of minimum-weight cycles of G is bounded above by a polynomial in the number of edges of G. A similar bound holds if we wish to count the number of cycles with weight at most a constant multiple of the minimum weight of a cycle of G.

Tidally compressed gas in centers of early-type and ultraluminous galaxies

In this paper we propose that the compressive tidal held in the centers of flat-core early-type galaxies and ultraluminous galaxies compresses molecular clouds producing dense gas observed in the centers of these galaxies. The effect of galactic tidal fields is usually considered disruptive in the literature. However, for some galaxies, the mass profile flattens toward the center and the resulting galactic tidal field is not disruptive, but instead it is compressive within the flat-core region. We have used the virial theorem to determine the minimum density of a molecular cloud to be stable and gravitationally bound within the tidally compressive region of a galaxy. We have applied the mechanism to determine the mean molecular cloud densities in the centers of a sample of flat-core, early-type galaxies and ultraluminous galaxies. For early-type galaxies with a core-type luminosity profile, the tidal held of the galaxy is compressive within half the core radius. We have calculated the mean gas densities for molecular gas in a sample of early-type galaxies which have already been detected in CO emission, and we obtain mean densities of [n] similar to 10(3)-10(6) cm(-3) within the central 100 pc radius. We also use our model to calculate the molecular cloud densities in the inner few hundred parsecs of a sample of ultraluminous galaxies. From the observed rotation curves of these galaxies we show that they have a compressive core within their nuclear region. Our model predicts minimum molecular gas densities in the range 10(2)-10(4) cm(-3) in the nuclear gas disks; the smaller values are applicable typically for galaxies with larger core radii. The resulting density values agree well with the observed range. Also, for large core radii, even fairly low-density gas (similar to 10(2) cm(-3)) can remain bound and stable close to the galactic center.

Implications of the half-duplex constraint on relay-aided cooperation using rateless codes

The half-duplex constraint, which mandates that a cooperative relay cannot transmit and receive simultaneously, considerably simplifies the demands made on the hardware and signal processing capabilities of a relay. However, the very inability of a relay to transmit and receive simultaneously leads to a potential under-utilization of time and bandwidth resources available to the system. We analyze the impact of the half-duplex constraint on the throughput of a cooperative relay system that uses rateless codes to harness spatial diversity and efficiently transmit information from a source to a destination. We derive closed-form expressions for the throughput of the system, and show that as the number of relays increases, the throughput approaches that of a system that uses more sophisticated full-duplex nodes. Thus, half-duplex nodes are well suited for cooperation using rateless codes despite the simplicity of both the cooperation protocol and the relays.

Half-sandwich (eta(6)-arene)ruthenium(II) chiral Schiff base complexes: Analysis of the diastereomeric mixtures in solution by 2D-NMR spectroscopy

2D NMR spectroscopy has been used to determine the metal configuration in solution of three complexes, viz. [(eta(6)-p-cymene)Ru(L*)Cl] (1) and [(eta(6)-p-cymene)Ru(L*)(L')] (ClO4) (L' = H2O, 2; PPh3, 3), where L* is the anion of (S)-(1-phenylethyl)salicylaldimine. The complexes exist in two diastereomeric forms in solution. Both the (R-Ru,S-C)- and (S-Ru,S-C)-diastereomers display the presence of attractive, CH/pi interaction involving the phenyl group attached to the chiral carbon and the cymene ring hydrogens. This interaction restricts the rotation of the C*-N single bond and, as a result, two structural types with either the hydrogen atom attached to the chiral carbon (C*) or the methyl group attached to C* in close proximity of the cymene ring protons get stabilized. Using 2D NMR spectroscopy as a tool, the spatial interaction involving these protons are studied in order to obtain the metal configuration(s) of the diastereomeric complexes in solution. This technique has enabled us to determine the metal configuration as (R-Ru,S-C) for the major isomers of 1-3 in solution.

Methods for making prisms with submultiple or half angles: applications to the measurement of the angles of Pechan and Pellin-Broca prisms

A simple technique is devised for making prisms with submultiple or half angles. As an application of these prisms, methods are suggested to measure the angles of the Pechan and Pellin-Broca prisms without using expensive spectrometers, autocollimators, and angle gauges. (C) 2002 Society of Photo-Optical Instrumentation Engineers.

Organometallic chemistry of diphosphazanes. Part 15. Half-sandwich cyclopentadienyl ruthenium complexes of achiral and chiral diphosphazanes

Reaction of [CpRu(PPh3)(2)Cl] (1) {Cp = eta(5)-(C5H5)} with X2PN(CHMe2) PYY' {X = Y = Y' = Ph (L-1); X = Y = Ph, Y' = OC6H4Me-4 (L-4); X = Y = Ph, Y' = OC6H3Me2- 3,5 (L-5); X = Y = Ph, Y' = N2C3HMe2 (L-6)} yields the cationic chelate complexes, [CpRu(eta(2)-(X2PN(CHMe2) PYY')) PPh3] Cl. On the other hand, the reaction of 1 with X2PN(CHMe2)PYY' {X = Ph, YY' = O2C6H4(L-3)} gives the complex, [CpRu(eta(1)-L-2)(2)PPh3] Cl. Both types of complexes are formed with X2PN(CHMe2) PYY' {X = Ph, YY' = O2C6H4 (L-3)}. The reaction of 1 with (R),(S)-(H12C20O2) PN(CHMe2) PPh2 (L-7) yields both cationic and neutral complexes, [CpRu{eta(2)-(L-7)} PPh3] Cl and [CpRu{eta(1)-(L-7)}(2)PPh3] Cl and [CpRu{eta(2)-(L-7)}Cl]. The reactions of optically pure diphosphazane, Ph2PN(*CHMePh) PPhY (Y = Ph (L-8); Y = N2C3HMe2-3,5 (L-9)) with 1 give the neutral and cationic ruthenium complexes, [CpRu{eta(2)-(Ph2PN(R) PPhY)} Cl] and [CpRu{eta(2)-(Ph2PN(R)PPhY)} PPh3] Cl. "Chiral-at-metal" ruthenium complexes of diphosphazanes have been synthesized with high diastereoselectivity. The absolute configuration of a novel ruthenium complex, (SCSPRRu)-[(eta(5)-C5H5) Ru*{eta(2)-(Ph2PN(*CHMePh)P*Ph( N2C3HMe2-3,5))} Cl] possessing three chiral centers, is established by X-ray crystallography. The reactions of [CpRu{eta(2)-(L-8)} Cl] with mono or diphosphanes in the presence of NH4PF6 yield the cationic complexes, [CpRu{eta(2)-(L-8)}{eta(1)-(P)}] PF6 {P = P(OMe)(3), PPh3, Ph2P(CH2)(n)PPh2 (n = 1 or 2)}.

Propargyloxycarbonyl (Poc) amino acid chlorides as efficient coupling reagents for the synthesis of 100% diastereopure peptides and resin bound tetrathiomolybdate as an effective deblocking agent for the Poc group

Synthesis of short peptides using propargyloxycarbonyl amino acid chlorides as effective coupling reagents and polymer supported tetrathiomolybdate as an efficient deblocking agent are reported.

A lower bound for the hitting set size for combinatorial rectangles and an application

We prove a lower bound of Omega(1/epsilon (m + log(d - a)) where a = [log(m) (1/4epsilon)] for the hitting set size for combinatorial rectangles of volume at least epsilon in [m](d) space, for epsilon is an element of [m(-(d-2)), 2/9] and d > 2. (C) 2002 Elsevier Science B.V. All rights reserved.

Axially homogeneous, zero mean flow buoyancy-driven turbulence in a vertical pipe

We report an experimental study of a new type of turbulent flow that is driven purely by buoyancy. The flow is due to an unstable density difference, created using brine and water, across the ends of a long (length/diameter=9) vertical pipe. The Schmidt number Sc is 670, and the Rayleigh number (Ra) based on the density gradient and diameter is about 108. Under these conditions the convection is turbulent, and the time-averaged velocity at any point is ‘zero’. The Reynolds number based on the Taylor microscale, Reλ, is about 65. The pipe is long enough for there to be an axially homogeneous region, with a linear density gradient, about 6–7 diameters long in the midlength of the pipe. In the absence of a mean flow and, therefore, mean shear, turbulence is sustained just by buoyancy. The flow can be thus considered to be an axially homogeneous turbulent natural convection driven by a constant (unstable) density gradient. We characterize the flow using flow visualization and particle image velocimetry (PIV). Measurements show that the mean velocities and the Reynolds shear stresses are zero across the cross-section; the root mean squared (r.m.s.) of the vertical velocity is larger than those of the lateral velocities (by about one and half times at the pipe axis). We identify some features of the turbulent flow using velocity correlation maps and the probability density functions of velocities and velocity differences. The flow away from the wall, affected mainly by buoyancy, consists of vertically moving fluid masses continually colliding and interacting, while the flow near the wall appears similar to that in wall-bound shear-free turbulence. The turbulence is anisotropic, with the anisotropy increasing to large values as the wall is approached. A mixing length model with the diameter of the pipe as the length scale predicts well the scalings for velocity fluctuations and the flux. This model implies that the Nusselt number would scale as Ra1/2Sc1/2, and the Reynolds number would scale as Ra1/2Sc−1/2. The velocity and the flux measurements appear to be consistent with the Ra1/2 scaling, although it must be pointed out that the Rayleigh number range was less than 10. The Schmidt number was not varied to check the Sc scaling. The fluxes and the Reynolds numbers obtained in the present configuration are much higher compared to what would be obtained in Rayleigh–Bénard (R–B) convection for similar density differences.