Glass Transition in the Density Functional Theory of Freezing

A mean-field description of the glass transition in the hard-sphere system is obtained by numerically locating "glassy" minima of a model free-energy functional. These minima, characterized by inhomogeneous but aperiodic density distributions, appear as the average density is increased above the value at which equilibrium crystallization takes place. Investigations of the density distribution and local bond-orientational order at these minima yield results similar to those obtained from simulations.

Diversity in Functional Organization of Class I and Class II Biotin Protein Ligase

The cell envelope of Mycobacterium tuberculosis (M. tuberculosis) is composed of a variety of lipids including mycolic acids, sulpholipids, lipoarabinomannans, etc., which impart rigidity crucial for its survival and pathogenesis. Acyl CoA carboxylase (ACC) provides malonyl-CoA and methylmalonyl-CoA, committed precursors for fatty acid and essential for mycolic acid synthesis respectively. Biotin Protein Ligase (BPL/BirA) activates apo-biotin carboxyl carrier protein (BCCP) by biotinylating it to an active holo-BCCP. A minimal peptide (Schatz), an efficient substrate for Escherichia coli BirA, failed to serve as substrate for M. tuberculosis Biotin Protein Ligase (MtBPL). MtBPL specifically biotinylates homologous BCCP domain, MtBCCP87, but not EcBCCP87. This is a unique feature of MtBPL as EcBirA lacks such a stringent substrate specificity. This feature is also reflected in the lack of self/promiscuous biotinylation by MtBPL. The N-terminus/HTH domain of EcBirA has the selfbiotinable lysine residue that is inhibited in the presence of Schatz peptide, a peptide designed to act as a universal acceptor for EcBirA. This suggests that when biotin is limiting, EcBirA preferentially catalyzes, biotinylation of BCCP over selfbiotinylation. R118G mutant of EcBirA showed enhanced self and promiscuous biotinylation but its homologue, R69A MtBPL did not exhibit these properties. The catalytic domain of MtBPL was characterized further by limited proteolysis. Holo-MtBPL is protected from proteolysis by biotinyl-59 AMP, an intermediate of MtBPL catalyzed reaction. In contrast, apo-MtBPL is completely digested by trypsin within 20 min of co-incubation. Substrate selectivity and inability to promote self biotinylation are exquisite features of MtBPL and are a consequence of the unique molecular mechanism of an enzyme adapted for the high turnover of fatty acid biosynthesis.

Electrooxidation of methanol in sulfuric-acid electrolyte on platized-carbon electrodes with several functional-group characteristics

The effect of acid/base functional-groups associated with platinized-carbon electrodes on their catalytic activity toward electro-oxidation of methanol in sulfuric acid electrolyte at 60-degrees-C is studied. Platinized-carbon electrodes with sm amounts of functional groups exhibit higher catalytic activity compared to those with large concentrations of acidic/basic surface functionalities. The overpotential for methanol oxidation is minimum on electrodes of platinized carbons with pHzpc values between 6 and 7. An x-ray photoelectron spectroscopic study of various platinized carbons suggests that the acid/base surface functional-groups produce ample amounts of surface Pt-oxides and a consequent decrease in activity toward methanol oxidation.

Ionic conductivity, mechanical strength and Li-ion battery performance of mono-functional and bi-functional (''Janus'') ``soggy sand'' electrolytes

Influence of dispersion of uniformly sized mono-functional and bi-functional (''Janus'') particles on ionic conductivity of novel ``soggy sand'' electrolytes and its implications on mechanical strength and lithium-ion battery performance are discussed here.

Establishment of the functional importance of thiamin carrier protein in pregnant rats by using monoclonal antibodies

Monoclonal antibodies (mAbs) to chicken thiamin carrier protein (TCP) have been produced by hybridoma technology to identify the crucial epitopes involved in bioneutralization of the vitamin carrier. The monoclonality of these mAbs (A4C4, F3H6, H8H3, C8C1 and G7H10) was sought to be confirmed by sub-class isotyping; they all belong to IgG1, k type. The epitopes recognized by all the five mAbs are conserved in TCP from the chicken to the rat as assessed by liquid phase RIA and immunoprecipitation of I-125-labelled proteins from pregnant rat serum. Among these mAbs, passive immunization of pregnant rats with the mAb C8C1 only on three consecutive days (day 10, 11 and 12) resulted in embryonic resorption. These results demonstrate the importance of epitopic structure specified by the mAb C8C1 on TCP during pregnancy in rats.

Functional analysis of conserved motifs in EcoP15I DNA methyltransferase

EcoP15I DNA methyltransferase recognizes the sequence 5'-CAGCAG-3' and transfers a methyl group to N-6 of the second adenine residue in the recognition sequence. All N-6 adenine methyltransferases contain two highly conserved sequences, FxGxG (motif I), postulated to form part of the S-adenosyl-L-methionine binding site and (D/N/S)PP(Y/F) (motif IV) involved in catalysis. We have altered the second glycine residue in motif I to arginine and serine, and substituted tyrosine in motif IV with tryptophan in EcoP15I DNA methyltransferase, using site-directed mutagenesis. The mutant enzymes were overexpressed, purified and characterized by biochemical methods. The mutations in motif I completely abolished AdoMet binding but left target DNA recognition unaltered. Although the mutation in motif IV resulted in loss of enzyme activity, we observed enhanced crosslinking of S-adenosyl-L-methionine and DNA. This implies that DNA and AdoMet binding sites are close to motif IV. Taken together, these results reinforce the importance of motif I in AdoMet binding and motif IV in catalysis. Additionally, limited proteolysis and UV crosslinking experiments with EcoP15I DNA methyltransferase imply that DNA binds in a cleft formed by two domains in the protein. Methylation protection analysis provides evidence for the fact that EcoP15I DNA MTase makes contacts in the major groove of its substrate DNA. Interestingly, hypermethylation of the guanine residue next to the target adenine residue indicates that the protein probably flips out the target adenine residue. (C) 1996 Academic Press Limited

Crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein MogA from two thermophilic organisms

Molybdenum-cofactor (Moco) biosynthesis is an evolutionarily conserved pathway in almost all kingdoms of life, including humans. Two proteins, MogA and MoeA, catalyze the last step of this pathway in bacteria, whereas a single two-domain protein carries out catalysis in eukaryotes. Here, three crystal structures of the Moco-biosynthesis protein MogA from the two thermophilic organisms Thermus thermophilus (TtMogA; 1.64 angstrom resolution, space group P2(1)) and Aquifex aeolicus (AaMogA; 1.70 angstrom resolution, space group P2(1) and 1.90 angstrom resolution, space group P1) have been determined. The functional roles and the residues involved in oligomerization of the protein molecules have been identified based on a comparative analysis of these structures with those of homologous proteins. Furthermore, functional roles have been proposed for the N- and C-terminal residues. In addition, a possible protein-protein complex of MogA and MoeA has been proposed and the residues involved in protein-protein interactions are discussed. Several invariant water molecules and those present at the subunit interfaces have been identified and their possible structural and/or functional roles are described in brief. In addition, molecular-dynamics and docking studies with several small molecules (including the substrate and the product) have been carried out in order to estimate their binding affinities towards AaMogA and TtMogA. The results obtained are further compared with those obtained for homologous eukaryotic proteins.

Reaction of diisopropoxytitanium(III) tetrahydroborate with selected organic compounds containing representative functional groups

Diisopropoxytitanium(III) tetrahydroborate, ((PrO)-Pr-1)(2)TiBH4), generated in situ in dichloromethane from diisopropoxytitanium dichloride and benzyltriethylammonium borohydride in a 1:2 ratio selectively reduces aldehydes, ketones, acid chlorides, carboxylic acids, and N-Boc-protected amino acids to the corresponding alcohols in excellent yield under very mild reaction conditions (-78 to 25 degrees C).

Primary Sequence That Determines the Functional Overlap between Mitochondrial Heat Shock Protein 70 Ssc1 and Ssc3 of Saccharomyces cerevisiae

The evolutionary diversity of the HSP70 gene family at the genetic level has generated complex structural variations leading to altered functional specificity and mode of regulation in different cellular compartments. By utilizing Saccharomyces cerevisiae as a model system for better understanding the global functional cooperativity between Hsp70 paralogs, we have dissected the differences in functional properties at the biochemical level between mitochondrial heat shock protein 70 (mtHsp70) Ssc1 and an uncharacterized Ssc3 paralog. Based on the evolutionary origin of Ssc3 and a high degree of sequence homology with Ssc1, it has been proposed that both have a close functional overlap in the mitochondrial matrix. Surprisingly, our results demonstrate that there is no functional cross-talk between Ssc1 and Ssc3 paralogs. The lack of in vivo functional overlap is due to altered conformation and significant lower stability associated with Ssc3. The substrate-binding domain of Ssc3 showed poor affinity toward mitochondrial client proteins and Tim44 due to the open conformation in ADP-bound state. In addition to that, the nucleotide-binding domain of Ssc3 showed an altered regulation by the Mge1 co-chaperone due to a high degree of conformational plasticity, which strongly promotes aggregation. Besides, Ssc3 possesses a dysfunctional inter-domain interface thus rendering it unable to perform functions similar to generic Hsp70s. Moreover, we have identified the critical amino acid sequence of Ssc1 and Ssc3 that can ``make or break'' mtHsp70 chaperone function. Together, our analysis provides the first evidence to show that the nucleotide-binding domain of mtHsp70s plays a critical role in determining the functional specificity among paralogs and orthologs across kingdoms.

Mutations in beta ` subunit of Escherichia coli RNA polymerase perturb the activator polymerase functional interaction required for promoter clearance

P>Transcription activator C employs a unique mechanism to activate mom gene of bacteriophage Mu. The activation process involves, facilitating the recruitment of RNA polymerase (RNAP) by altering the topology of the promoter and enhancing the promoter clearance by reducing the abortive transcription. To understand the basis of this multi-step activation mechanism, we investigated the nature of the physical interaction between C and RNAP during the process. A variety of assays revealed that only DNA-bound C contacts the beta' subunit of RNAP. Consistent to these results, we have also isolated RNAP mutants having mutations in the beta' subunit which were compromised in C-mediated activation. Mutant RNAPs show reduced productive transcription and increased abortive initiation specifically at the C-dependent mom promoter. Positive control (pc) mutants of C, defective in interaction with RNAP, retained the property of recruiting RNAP to the promoter but were unable to enhance promoter clearance. These results strongly suggest that the recruitment of RNAP to the mom promoter does not require physical interaction with C, whereas a contact between the beta' subunit and the activator, and the subsequent allosteric changes in the active site of the enzyme are essential for the enhancement of promoter clearance.

Functional Significance of an Evolutionarily Conserved Alanine (GCA) Resume Codon in tmRNA in Escherichia coli

Occasionally, ribosomes stall on mRNAs prior to the completion of the polypeptide chain. In Escherichia coli and other eubacteria, tmRNA-mediated trans-translation is a major mechanism that recycles the stalled ribosomes. The tmRNA possesses a tRNA-like domain and a short mRNA region encoding a short peptide (ANDENYALAA in E. coli) followed by a termination codon. The first amino acid (Ala) of this peptide encoded by the resume codon (GCN) is highly conserved in tmRNAs in different species. However, reasons for the high evolutionary conservation of the resume codon identity have remained unclear. In this study, we show that changing the E. coli tmRNA resume codon to other efficiently translatable codons retains efficient functioning of the tmRNA. However, when the resume codon was replaced with the low-usage codons, its function was adversely affected. Interestingly, expression of tRNAs decoding the low-usage codon from plasmid-borne gene copies restored efficient utilization of tmRNA. We discuss why in E. coli, the GCA (Ala) is one of the best codons and why all codons in the short mRNA of the tmRNA are decoded by the abundant tRNAs.

Manipulation of the Hydration Levels in Minerals of Sodium Cadmium Bisulfate toward the Design of Functional Materials

Several variants of hydrated sodium cadmium bisulfate, Na(2)Cd(2)(SO(4))(3) center dot 3H(2)O, Na(2)Cd(SO(4))(2) center dot 2H(2)O, and Na(2)Cd(SO(4))(2) center dot 4H(2)O have been synthesized, and their thermal properties followed by phase transitions have been invesigated. The formation of these phases depends on the stochiometry and the time taken for crystallization from water. Na(2)Cd(2)(SO(4))(3)center dot 3H(2)O, which crystallizes in the trigonal system, space group P3c, is grown from the aqueous solution in about four weeks. The krohnkite type mineral Na(2)Cd(SO(4))(2) center dot 2H(2)O and the mineral astrakhanite, also known as blodite, Na(2)Cd (SO(4))(2)center dot 4H(2)O, crystallize concomittantly in about 24 weeks. Both these minerals belong to the monoclinic system(space group P2(1)/c). Na(2)Cd(2)(SO(4))(3)center dot 3H(2)O loses water completely when heated to 250 degrees C and transforms to a dehydrated phase (cubic system, space group I (4) over bar 3d) whose structure has been established using ab initio powder diffration techniques. Na(2)Cd(SO(4))(2)center dot 2H(2)O transforms to alpha-Na(2)Cd(SO(4))(2) (space group C2/c) on heating to 150 degrees C which is a known high ionic conductor and remains intact over prolonged periods of exposure to moisture (over six months). However, when alpha-Na(2)Cd(SO(4))(2) is heated to 570 degrees C followed by sudden quenching in liquid nitrogen beta-Na(2)Cd(SO(4))(2) (P2(1)/c) is formed. beta-Na(2)Cd(SO(4))(2) takes up water from the atmosphere and gets converted completely to the krohnkite type mineral in about four weeks. Further, beta-Na(2)Cd(SO(4))(2) has a conductivity behavior comparable to the a-form up to 280 degrees C, the temperature required for the transformation of the beta- to alpha-form. These experiments demonstrate the possibility of utilizing the abundantly available mineral sources as precursors to design materials with special properties.

Surfactant-mediated Synthesis of Functional Metal Oxide Nanostructures via Microwave Irradiation-assisted Chemical Synthesis

Nanostructured materials have attracted considerable interest in recent years due to their properties which differ strongly from their bulk phase and potential applications in nanoscale electronic and optoelectronic devices. Metal oxide nanostructures can be synthesized by variety of different synthesis techniques developed in recent years such as thermal decomposition, sol-gel technique, chemical coprecipitation, hydrothermal process, solvothermal process, spray pyrolysis, polyol process etc. All the above processes go through a tedious synthesis procedure followed by prolonged heat treatment at elevated temperature and are time consuming. In the present work we describe a rapid microwave irradiation-assisted chemical synthesis technique for the growth of nanoparticles, nanorods, and nanotubes of a variety of metal oxides in the presence of an appropriate surfactant, without the use of any templates The method is simple, inexpensive, and helps one to prepare nanostructures in a very simple way, and in a very short time, measured in minutes. The synthesis procedure employs high quality metalorganic complexes (typically -diketonates) featuring a direct metal-to-oxygen bond in its molecular structure. The complex is dissolved in a suitable solvent, often with a surfactant added, and the solution then subjected to microwave irradiation in a domestic microwave oven operating at 2.45 GHz frequency with power varying from 160-800 W, from a few seconds to a few minutes, leading to the formation of corresponding metal oxides. This method has been used successfully to synthesize nanostructures of a variety of binary and ternary metal oxides such as ZnO, CdO, Fe2O3, CuO, Ga2O3, Gd2O3, ZnFe2O4, etc. There is an observed variation in the morphology of the nanostructures with the change of different parameters such as microwave power, irradiation time, appropriate solvent, surfactant type and concentration. Cationic, anionic, nonionic and polymeric surfactants have been used to generate a variety of nanostructures. Even so, to remove the surfactant, there is either no need of heat treatment or a very brief exposure to heat suffices, to yield highly pure and crystalline oxide materials as prepared. By adducting the metal complexes, the shape of the nanostructures can be controlled further. In this manner, very well formed, single-crystalline, hexagonal nanorods and nanotubes of ZnO have been formed. Adducting the zinc complex leads to the formation of tapered ZnO nanorods with a very fine tip, suitable for electron emission applications. Particle size and their monodispersity can be controlled by a suitable choice of a precursor complex, the surfactant, and its concentration. The resulting metal oxide nanostructures have been characterized by X-ray diffraction, field emission scanning electron microscopy, transmission electron microscopy, FTIR spectroscopy, photoluminescence, and electron emission measurements.