Effect of Substrate Binding Loop Mutations on the Structure, Kinetics, and Inhibition of Enoyl Acyl Carrier Protein Reductase from Plasmodium falciparum

Enoyl acyl carrier protein reductase (ENR), which catalyzes the final and rate limiting step of fatty acid elongation, has been validated as a potential drug target. Triclosan is known to be an effective inhibitor for this enzyme. We mutated the substrate binding site residue Ala372 of the ENR of Plasmodium falciparum (PfENR) to Methionine and Valine which increased the affinity of the enzyme towards triclosan to almost double, close to that of Escherichia coli ENR (EcENR) which has a Methionine at the structurally similar position of Ala372 of PfENR. Kinetic studies of the mutants of PfENR and the crystal structure analysis of the A372M mutant revealed that a more hydrophobic environment enhances the affinity of the enzyme for the inhibitor. A triclosan derivative showed a threefold increase in the affinity towards the mutants compared to the wild type, due to additional interactions with the A372M mutant as revealed by the crystal structure. The enzyme has a conserved salt bridge which stabilizes the substrate binding loop and appears to be important for the active conformation of the enzyme. We generated a second set of mutants to check this hypothesis. These mutants showed loss of function, except in one case, where the crystal structure showed that the substrate binding loop is stabilized by a water bridge network. (C) 2011 IUBMB mum Life, 63(1): 30-41,2011

Hydrodynamics of R-charged D1-branes

We study the hydrodynamic properties of strongly coupled SU(N) Yang-Mills theory of the D1-brane at finite temperature and at a non-zero density of R-charge in the framework of gauge/gravity duality. The gravity dual description involves a charged black hole solution of an Einstein-Maxwell-dilaton system in 3 dimensions which is obtained by a consistent truncation of the spinning D1-brane in 10 dimensions. We evaluate thermal and electrical conductivity as well as the bulk viscosity as a function of the chemical potential conjugate to the R-charges of the D1-brane. We show that the ratio of bulk viscosity to entropy density is independent of the chemical potential and is equal to 1/4 pi. The thermal conductivity and bulk viscosity obey a relationship similar to the Wiedemann-Franz law. We show that at the boundary of thermodynamic stability, the charge diffusion mode becomes unstable and the transport coefficients exhibit critical behaviour. Our method for evaluating the transport coefficients relies on expressing the second order differential equations in terms of a first order equation which dictates the radial evolution of the transport coefficient. The radial evolution equations can be solved exactly for the transport coefficients of our interest. We observe that transport coefficients of the D1-brane theory are related to that of the M2-brane by an overall proportionality constant which sets the dimensions.

Inefficient excision of uracil from loop regions of DNA oligomers by E.coli uracil DNA glycosylase

Kinetic parameters for uracil DNA glycosylase (E.coli)-catalysed excision of uracil from DNA oligomers containing dUMP in different structural contexts were determined. Our results show that single-stranded oligonucleotides (unstructured) are used as somewhat better substrates than the double-stranded oligonucleotides. This is mainly because of the favourable V-max value of the enzyme for single-stranded substrates. More interestingly, however, we found that uracil release from loop regions of DNA hairpins is extremely inefficient. The poor efficiency with which uracil is excised from loop regions is a result of both increased K-m and lowered V-max values. This observation may have significant implications in uracil DNA glycosylase-directed repair of DNA segments that can be extruded as hairpins. In addition, these studies are useful in designing oligonucleotides for various applications in DNA research where the use of uracil DNA glycosylase is sought.

Perturbative corrections for staggered four-fermion operators

We present results for one-loop matching coefficients between continuum four-fermion operators, defined in the Naive Dimensional Regularization scheme, and staggered fermion operators of various types. We calculate diagrams involving gluon exchange between quark fines, and ''penguin'' diagrams containing quark loops. For the former we use Landau-gauge operators, with and without O(a) improvement, and including the tadpole improvement suggested by Lepage and Mackenzie. For the latter we use gauge-invariant operators. Combined with existing results for two-loop anomalous dimension matrices and one-loop matching coefficients, our results allow a lattice calculation of the amplitudes for KKBAR mixing and K --> pipi decays with all corrections of O(g2) included. We also discuss the mixing of DELTAS = 1 operators with lower dimension operators, and show that, with staggered fermions, only a single lower dimension operator need be removed by non-perturbative subtraction.

Primary structure of sesbania mosaic virus coat protein: its implications to the assembly and architecture of the virus

Sesbania mosaic virus (SMV) is a plant virus that infects Sesbania grandiflora plants in Andhra Pradesh, India. The amino acid sequence of the coat protein of SMV was determined using purified peptides generated by cleavage with trypsin, chymotrypsin, V8 protease and clostripain. The 230 residues so far determined were compared to the corresponding residues of southern bean mosaic virus (SBMV), the type member of sobemoviruses. The overall identity between the sequences is 61.7%. The amino terminal 64 residues, which constitute an independent domain (R-domain) known to interact with RNA, are conserved to a lower extent (52.5%). Comparison of the positively charged residues in this domain suggests that the RNA-protein interactions are considerably weaker in SMV. The residues that constitute the major domain of the coat protein, the surface domain (S-domain, residues 65-260), are better conserved (66.5%). The positively charged residues of this domain that face the nucleic acid are well conserved. The longest conserved stretch of residues (131-142) corresponds to the loop involved in intersubunit interactions between subunits related by the quasi 3-fold symmetry. A unique cation binding site located on the quasi 3-fold axis contributes to the stability of SMV. These differences are reflected in the increased stability of the SMV coat protein and its ability to be reconstituted with RNA at pH 7.5. A major epitope was identified using monoclonal antibodies to SMV in the segment 201-223 which contains an exposed helix in the capsid structure. This region is highly conserved between SMV and SBMV (70%) suggesting that it could represent the site of an important function such as vector recognition.

Bloch-Nordsieck thermometers: One-loop exponentiation in finite temperature QED

We study the scattering of hard external particles in a heat bath in a real-time formalism for finite temperature QED. We investigate the distribution of the 4-momentum difference of initial and final hard particles in a fully covariant manner when the scale of the process, Q, is much larger than the temperature, T. Our computations are valid for all T subject to this constraint. We exponentiate the leading infra-red term at one-loop order through a resummation of soft (thermal) photon emissions and absorptions. For T > 0, we find that tensor structures arise which are not present at T = 0. These carry thermal signatures. As a result, external particles can serve as thermometers introduced into the heat bath. We investigate the phase space origin of log (Q/M) and log (Q/T) terms.

Enantioselective synthesis of both (+)- and (-)-derivatives of bicyclo[4.3.0]nonan-8-one and 3,8-diones from R-carvone

Enantioselective synthesis of both the enantiomeric forms of the hydrindane derivatives mentioned in the title, potential chiral precursors in terpenoid synthesis, starling from R-carvone employing two different cyclopentannulation methodologies is described.

Structure of N-nitroso-r-2,c-7-diphenylhexahydro-1,4-diazepin-5-one

C17H17N3O2, M(r) = 295.34, orthorhombic, P2(1)2(1)2(1), a = 7.659 (1), b = 12.741 (1), c = 15.095 (1) angstrom, V = 1473.19 (2) angstrom 3, Z = 4, D(m) = 1.33, D(x) = 1.32 Mg m-3, lambda(Cu K-alpha) = 1.5418 angstrom, mu = 0.68 mm-1, F(000) = 624, T = 295 K, R = 0.031 for 1549 unique observed reflections with I > 2.5-sigma(I). The seven-membered heterocyclic ring adopts a boat conformation flattened at the nitroso end of the ring. The substituent phenyl rings occupy pseudo-axial positions and the nitroso group is coplanar with the C(2), N(1), C(7) plane of the central ring. The crystal structure is stabilized by intermolecular N-H...O and weak C-H...O hydrogen bonds.

Organometallic chemistry of diphosphazanes. Rhodium(I) complexes of RN(PX2)2 (R = C6H5; X = OC6H5, OC6H4Br?p, R = CH3; X = OC6H5)

Reactions of [Rh(COD)Cl](2) with the ligand RN(PX(2))(2) (1: R=C6H5; X=OC6H5) give mono- or disubstituted complexes of the type [Rh-2(COD)Cl-2{eta(2)-C6H5N(P(OC6H5)(2))(2)}-] or [RhCl{eta(2)-C6H5N(P(OC6H5)(2))(2)}](2), depending on the reaction conditions. Reaction of 1 with [Rh(CO)(2)Cl](2) gives the symmetric binuclear complex, [Rh(CO)Cl{mu-C6H5N(P(OC6H5)(2))(2)}], whereas the same reaction with 2 (R=CH3; X=OC6H5) leads to the formation of an asymmetric complex of the type [Rh(CO)(mu-CO)Cl{mu-CH3N(P(OC6H5)(2))(2)}] containing both terminal and bridging CO groups. Interestingly the reaction of 3 (R=C6H5, X = OC6H4Br-p) with either [Rh(COD)Cl](2) or [Rh(CO)(2)Cl](2) leads only to the formation of the chlorine bridged binuclear complex, [RhCl{eta(2)-C6H5N(P(OC6H4Br-p)(2))(2)}](2). The structural elucidation of the complexes was carried out by elemental analyses, IR and P-31 NMR spectroscopic data.

Structural and optical properties of nonpolar (11-20) a-plane GaN grown on (1-102) r-plane sapphire substrate by plasma-assisted molecular beam epitaxy

We report the structural and optical properties of a-plane GaN film grown on r-plane sapphire substrate by plasma-assisted molecular beam epitaxy. High resolution X-ray diffraction was used to determine the out-of-plane and in-plane epitaxial relation of a-plane GaN to r-plane sapphire. Low-temperature photoluminescence emission was found to be dominated by basal stacking faults along with near-band emission. Raman spectroscopy shows that the a-GaN film is of reasonably good quality and compressively strained. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Spin-Selective Correlation Experiment for Measurement of Long-Range J Couplings and for Assignment of (R/S) Enantiomers from the Residual Dipolar Couplings and DFT

We report the C-HETSERF experiment for determination of long- and short-range homo- and heteronuclear scalar couplings ((n)J(HH) and (n)J(XH), n >= 1) of organic molecules with a low sensitivity dilute heteronucleus in natural abundance. The method finds significant advantage in measurement of relative signs of long-range heteronuclear total couplings in chiral organic liquid crystal. The advantage of the method is demonstrated for the measurement of residual dipolar couplings (RDCs) in enantiomers oriented in the chiral liquid crystal with a focus to unambiguously assign R/S designation in a 2D spectrum. The alignment tensor calculated from the experimental RDCs and with the computed structures of enantiomers obtained by DFT calculations provides the size of the back-calculated RDCs. Smaller root-mean-square deviations (rmsd) between experimental and calculated RDCs indicate better agreement with the input structure and its correct designation of the stereogenic center.

Mechanism of “Autoacceleration” in the Thermal Oxidative Polymerization of R-Methylstyrene

Thermal oxidative polymerization of alpha-methylstyrene (AMS) has been studied at various temperatures(45-70 degrees C) and pressures (50-400 psi). Due to its high electron dense double bond, it undergoes thermal oxidative polymerization even at low temperatures fairly easily. The major products are poly(alpha-methylstyrene peroxide) (PMSP), and its decomposition products are acetophenone and formaldehyde. Above 45 degrees C the rate of polymerization increases sharply at a particular instant showing an ''autoacceleration'' with the formation of a knee point. The ''autoacceleration'' is supported from the fact that the plot, of R-p vs T shows a rapid rise, and the plot of ln R-p vs 1/T is non-Arrhenius. The occurrence of autoacceleration is explained on the basis of acetophenone-induced cleavage of PMSP during polymerization, generating more initiating alkoxy radicals, which subsequently leads to the rapid rise in the rate of polymerization. The mechanism of autoacceleration is supported by the change in. order, activation energy, and activation volume before and after the knee point.

R-parity violation in neutralino decays at an e gamma collider

At an e gamma collider, a selectron (e) over tilde(L,R) may be produced in association with a (lightest) neutralino <(chi)over tilde>(0)(1). Decay of the selectron may be expected to yield a final state with an electron and another <(chi)over tilde>(0)(1). If R-parity is violated, these two neutralinos will decay, giving rise to distinctive signatures, which are identified and studied. (C) 1998 Published by Elsevier Science B.V.

Structure of basic winged-bean lectin and a comparison with its saccharide-bound form

The crystal structure of the saccharide-free form of the basic form of winged-bean agglutinin (WBAI) has been solved by the molecular-replacement method and refined at 2.3 Angstrom resolution The final R factor is 19.74b for all data in the resolution range 8.0-2.3 Angstrom. The asymmetric unit contains two half-dimers, each located on a crystallographic twofold axis. The structure of the saccharide-free form is compared with that of the complex of WBAI wi th methyl-alpha-D-galactoside. The complex is composed of two dimers in the asymmetric unit. The intersubunit interactions in the dimer are nearly identical in the two structures The binding site of the saccharide-free structure contains three ordered water molecules at positions similar to those of the hydroxyl groups of the carbohydrate which an hydrogen bonded to the protein. Superposition of the saccharide-binding sites of the two structures shows that the major changes involve expulsion of these ordered water molecules and a shift of about 0.6 Angstrom of the main-chain atoms of the variable loop.