On the importance of backbone loop and peptide flip in the Walker sequence in F-1-ATPase action

The Walker sequence, GXXXXGKT, present in all the six subunits of F-1-ATPase exists in a folded form, known as phosphate-binding loop (P-loop). Analysis of the Ramachandran angles showed only small RMS deviation between the nucleotide-bound and nucleotide-free forms. This indicated a good overlap of the backbone loops. The catalytic beta-subunits (chains D, E and F) showed significant changes in the Ramachandran angles and the side chain torsion angles, but not the structural alpha-subunits (chains A, B and C). Most striking among these are the changes associated with Val160 and Gly161 corresponding to a flip in the peptide unit between them when a nucleotide is bound (chains D or F compared to nucleotide-free chain E). The conformational analysis further revealed a hitherto unnoticed hydrogen bond between amide-N of the flipped Gly161 and terminal phosphate-O of the nucleotide. This assigns a role for this conserved amino acid, otherwise ignored, of making an unusual direct interaction between the peptide backbone of the enzyme protein and the incoming nucleotide substrate. Significance of this interaction is enhanced, as it is limited only to the catalytic subunits, and also likely to involve a mechanical rotation of bonds of the peptide unit. Hopefully this is part of the overall events that link the chemical hydrolysis of ATP with the mechanical rotation of this molecule, now famous as tiny molecular motor.

Organically templated linear and layered cadmium sulfates

By reacting cadmium salts with H2SO4 in the presence of organic amines or directly with amine sulfates under hydrothermal conditions, it has been possible to prepare three linear cadmium sulfates of linarite topology, with the compositions [H3N(CH2)(2)NH3](2)[CdCl2(SO4)][SO4].H2O, I, [HN(CH2)(6)NH][CdBr2(SO4)], II, [HN(CH2)(6)NH][CdCl2-(SO4)], III. A layered cadmium sulfate of composition [H3N(CH2)(3)NH3][Cd-2(H2O)(2)(SO4)(3)], IV, has also been obtained. These sulfates are the first examples of a family of organically templated metal sulfates with interesting structural features. In the linarite chains, the CdX4O2 (X = Cl, Br) octahedron shares two trans-edges to form an [Mphi(4)] (phi = anionic ligand) chain decorated by the SO4 tetrahedron that adopts a staggered arrangement on either side of the chain. IV is constructed by the fusion of four-membered ring ladders involving edge sharing between the sulfate tetrahedron and metal octahedron. IV appears to be the first member of a family of organically templated metal sulfates containing an octahedral-tetrahedral 2D net wherein the sulfate tetrahedron is connected at all four corners.

Synthesis of novel cationic lipids with fully or partially non-scissile linkages between the hydrocarbon chains and pseudoglyceryl backbone

Five novel cationic lipids with fully or partially non-scissile linkage regions between the pseudoglyceryl backbone and the hydrocarbon chains have been synthesized. The membrane-forming properties of these new lipids are briefly presented.

Synthesis of phospholipids with fatty acid chains containing aromatic units at various depths

A series of diacyl phosphatidylcholine lipid derivatives, which contain aromatic units at various depths of their fatty acid chains, have been synthesized. These lipids produced stable aqueous suspensions. Electron microscopy revealed the presence of vesicular aggregates in the suspensions of these newly synthesized lipids. These membranes were oxidatively stable and maintained fluid character at ambient temperature making them ideal candidates for membrane protein reconstitution studies.

Grain Floatation During Equiaxed Solidification of an Al-Cu Alloy in a Side-Cooled Cavity: Part II-Numerical Studies

In this article, a single-phase, one-domain macroscopic model is developed for studying binary alloy solidification with moving equiaxed solid phase, along with the associated transport phenomena. In this model, issues such as thermosolutal convection, motion of solid phase relative to liquid and viscosity variations of the solid-liquid mixture with solid fraction in the mobile zone are taken into account. Using the model, the associated transport phenomena during solidification of Al-Cu alloys in a rectangular cavity are predicted. The results for temperature variation, segregation patterns, and eutectic fraction distribution are compared with data from in-house experiments. The model predictions compare well with the experimental results. To highlight the influence of solid phase movement on convection and final macrosegregation, the results of the current model are also compared with those obtained from the conventional solidification model with stationary solid phase. By including the independent movement of the solid phase into the fluid transport model, better predictions of macrosegregation, microstructure, and even shrinkage locations were obtained. Mechanical property prediction models based on microstructure will benefit from the improved accuracy of this model.

Grain Floatation During Equiaxed Solidification of an Al-Cu Alloy in a Side-Cooled Cavity: Part I-Experimental Studies

Experimental studies were performed to investigate the role and influence of grain movement on macrosegregation and microstructure evolution during equiaxed solidification. Casting experiments were performed with a grain-refined Al-Cu alloy in a rectangular sand mold. For the aluminum alloy studied, the equiaxed grains are lighter than the bulk melt and thus float up. Experiments were designed to investigate floatation phenomena of equiaxed grains in the presence of thermosolutal convection. Cooling curves were recorded at key locations in both the casting and the chill. Quantitative image analysis and spatial chemical analysis were performed on the solidified casting to observe the chemical and microstructural inhomogeneity created by the melt convection and solid floatation. Several notable features that can be attributed to grain movement were observed in temperature histories, macrosegregation patterns, and microstructures. In our experiments, the floatation of grains influences the thermal conditions and the overall flow direction in the casting cavity. In some cases, the induced flow resulting from the grain movement caused a flow reversal. This in turn influences the solidification direction, microstructure evolution, and the overall macrosegregation behavior.

Synthesis and Properties of a Novel (Main-Chain)– (Side-Chain) Polymeric Peroxide

A novel (main-chain)-(side-chain) vinyl polyperoxide, poly(dipentene peroxide)(PDP), an alternating copolymer of dipentene (DP) and oxygen, has been synthesized by thermal oxidative polymerization of DP. The PDP was characterized by 1H NMR, 13C NMR, FTIR, DSC, TGA, and EI-MS studies. The overall activation energies of the degradation from Kissinger’s method were 28 and 33 kcal/mol, respectively, for the endocyclic and acyclic peroxide units. The side-chain peroxy groups were found to be thermally more stable than the main chain. Above 45°C the rate of polymerization increases sharply at a particular instant showing an “autoacceleration” with the formation of knee point. The kinetics of autoacceleration has been studied at various temperatures (45–70°C) and pressures (50–250 psi). © 2000 John Wiley&Sons, Inc. J Appl Polym Sci 79: 1549–1555, 2001

Two-channel Kondo physics in odd impurity chains

We study odd-membered chains of spin-1/2 impurities, with each end connected to its own metallic lead. For antiferromagnetic exchange coupling, universal two-channel Kondo (2CK) physics is shown to arise at low energies. Two overscreening mechanisms are found to occur depending on coupling strength, with distinct signatures in physical properties. For strong interimpurity coupling, a residual chain spin-1/2 moment experiences a renormalized effective coupling to the leads, while in the weak-coupling regime, Kondo coupling is mediated via incipient single-channel Kondo singlet formation. We also investigate models in which the leads are tunnel-coupled to the impurity chain, permitting variable dot filling under applied gate voltages. Effective low-energy models for each regime of filling are derived, and for even fillings where the chain ground state is a spin singlet, an orbital 2CK effect is found to be operative. Provided mirror symmetry is preserved, 2CK physics is shown to be wholly robust to variable dot filling; in particular, the single-particle spectrum at the Fermi level, and hence the low-temperature zero-bias conductance, is always pinned to half-unitarity. We derive a Friedel-Luttinger sum rule and from it show that, in contrast to a Fermi liquid, the Luttinger integral is nonzero and determined solely by the ``excess'' dot charge as controlled by gate voltage. The relevance of the work to real quantum dot devices, where interlead charge-transfer processes fatal to 2CK physics are present, is also discussed. Physical arguments and numerical renormalization-group techniques are used to obtain a detailed understanding of these problems.

Beta-structure of polypeptides in non-aqueous solutions. II. Side-chain orientation

The specific side-chain orientations of the phenyl group in the polypeptides poly-S-benzyl-L-cysteine, poly-S-carbobenzoxy-L-cysteine and poly-O-carbobenzoxy-L-serine in the beta-structure have been studied by spectral measurements in solutions. All the three polypeptides exhibit aromatic CD bands, indicating the asymmetric placement of the side-chain phenyl rings when the polypeptide backbone takes up the antiparallel beta-structure. Supporting evidence for this is derived from n.m.r. spectra of the polypeptides, which show upfield shift of the phenyl protons due to the stacking of the aromatic rings. Molecular model building studies reveal the stacking of alternate phenyl groups along the polypeptide chain.

Ferrocene-Conjugated L-Tryptophan Copper(II) Complexes of Phenanthroline Bases Showing DNA Photocleavage Activity and Cytotoxicity

Ferrocene-conjugated L-tryptophan (L-Trp) reduced Schiff base (Fc-TrpH) copper(II) complexes [Cu(Fc-Trp)(L)](ClO(4)) of phenanthroline bases (L), viz. 2,2'-bipyridine (bpy in 1), 1,10-phenanthroline (phen in 2), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq in 3), and dipyrido[3,2-a:2',3'-c]phenazine (dppz in 4), were prepared and characterized and their photocytotoxicity studied. Cationic reduced Schiff base (Ph-TrpH) complexes [Cu(Ph-Trp)(L)(H(2)O)] (ClO(4)) (L = phen in 5; dppz in 6) having the ferrocenyl moiety replaced by a phenyl group and the Zn(II) analogue (7) of complex 4 were prepared and used as control species. The crystal structures of 1 and 5 with respective square-planar CuN(3)O and square-pyramidal CuN(3)O(2) coordination geometry show significantly different core structures. Complexes 1-4 exhibit a Cu(II)-Cu(I) redox couple near -0.1 V and the Fc(+)-Fc couple at similar to 0.5 V vs SCE in DMF-0.1 M [Bu(4)(n)N] (ClO(4)) (Fc = ferrocenyl moiety). The complexes display a copper(II)-based d-d band near 600 nm and a Fc-centered band at similar to 450 nm in DMF-Tris-HCl buffer. The complexes are efficient binders to calf thymus DNA. They are synthetic chemical nucleases in the presence of thiol or H(2)O(2), forming hydroxyl radicals. The photoactive complexes are cleavers of pUC19 DNA in visible light, forming hydroxyl radicals. Complexes 2-6 show photocytotoxicity in HeLa cancer cells, giving IC(50) values of 4.7, 10.2, 1.3, 4.8, and 4.3 mu M, respectively, in visible light with the appearance of apoptotic bodies. The complexes also show photocytotoxicity in MCF-7 cancer cells. Nuclear chromatin cleavage has been observed with acridine orange/ethidium bromide (AO/EB) dual staining with complex 4 in visible light. The complexes induce caspase-independent apoptosis in the HeLa cells.

Conformational studies of the phosphazenyl side chain in cyclophosphazenes. Part 3. Crystal and molecular structure of N3P3Cl4(NEt2)(NPPh3)

The crystal structure of N3P3Cl4(NEt2)(NPPh3) has been determined. The crystals are orthorhombic, space group Pbca, with a= 8.208(1), b= 21.890(1), c= 31.722(2)Å, Z= 8, and m.p. = 146.5 °C. The structure was solved by direct methods and refined to a final R value of 0.045 for 2 025 independent reflections. The analysis reveals significant variations in the ring P–N bond lengths. The two nitrogenous substituents, NPPh3 and NEt2, reside on the same phosphorus atom. The latter, NEt2, has an almost exact type II conformation (the plane NC2 almost perpendicular to the local NPN plane)(the first observed for a dialkylamino-group in cyclophosphazenes), the former, NPPh3, deviates from type II towards type III (in type III the plane Pring–N–Pexo makes an angle of ca. 45° with the local N–P–N ring plane). The present structure is compared with others of triphenylphosphazenyl-cyclophosphazenes and the conformation of the NPPh3 substituent and its electron supply in the ground and perturbed states are discussed.

Tryptophan-water interaction in Monellin:Hydration patterns from molecular dynamics simulations

Femtosecond spectroscopy carried out earlier on Monellin and some other systems has given insights into the hydration dynamics of the proteins. In the present work, molecular dynamics simulations have been performed on Monellin to study the hydration dynamics. A method has been described to follow up the molecular events of the protein–water interactions in detail. The time constants of the survival correlation function match well with the reported experimental values. This validates the procedure, adapted here for Monellin, to investigate the hydration dynamics in general.

Lossy distribution source coding with side information

In a typical sensor network scenario a goal is to monitor a spatio-temporal process through a number of inexpensive sensing nodes, the key parameter being the fidelity at which the process has to be estimated at distant locations. We study such a scenario in which multiple encoders transmit their correlated data at finite rates to a distant and common decoder. In particular, we derive inner and outer bounds on the rate region for the random field to be estimated with a given mean distortion.

Analysis of LDPC Codes for Compression of Nonuniform Sources with Side Information Using Density Evolution

In this paper, we explore the use of LDPC codes for nonuniform sources under distributed source coding paradigm. Our analysis reveals that several capacity approaching LDPC codes indeed do approach the Slepian-Wolf bound for nonuniform sources as well. The Monte Carlo simulation results show that highly biased sources can be compressed to 0.049 bits/sample away from Slepian-Wolf bound for moderate block lengths.