The role of water in the catalytic efficiency of triosephosphate isomerase

The structural basis for the effect of the S96P mutation in chicken triosephosphate isomerase (cTIM) has been analyzed using a combination of X-ray crystallography and Fourier transform infrared spectroscopy. The X-ray structure is that of the enzyme complexed with phosphoglycolohydroxamate (PGH), an intermediate analogue, solved at a resolution of 1.9 A. The S96P mutation was identified as a second-site reverent when catalytically crippled mutants, E165D and H95N, were subjected to random mutagenesis. The presence of the second mutation leads to enhanced activity over the single mutation. However, the effect of the S96P mutation alone is to decrease the catalytic efficiency of the enzyme. The crystal structures of the S96P double mutants show that this bulky proline side chain alters the water structure within the active-site cavity (E165D; ref 1) and prevents nonproductive binding conformations of the substrate (H95N; ref 2). Comparison of the S96P single mutant structure with those of the wild-type cTIM, those of the single mutants (E165D and H95N), and those of the double mutants (E165D/S96P and H95N/S96P) begins to address the role of the conserved serine residue at this position. The results indicate that the residue positions the catalytic base E165 optimally for polarization of the substrate carbonyl, thereby aiding in proton abstraction. In addition, this residue is involved in positioning critical water molecules, thereby affecting the way in which water structure influences activity.     

The embryology ofStegnospermataceae,with a discussion on its status,affinities and systematic position

The embryology ofStegnosperma halimifolium andS. watsonii has been studied in detail. The tapetum is of the secretory type and its cells become multinucleate. Simultaneous cytokinesis in the pollen mother cells follows meiosis. The ripe pollen grains are 3-celled. The ovule is crassinucellate, bitegmic and amphitropous, with the micropyle formed by the inner integument alone. The female archesporium is one celled, and the parietal tissue 3–5 layered. The embryo sac development conforms to thePolygonum type. A central strand, 6 or 7 cells thick, differentiates inside the nucellus and extends from the base of the embryo sac to the chalazal region. The endosperm is nuclear. The embryogeny conforms to the Caryophyllad type. The seed coat is formed by the outer epidermis of the outer integument and the inner epidermis of the inner integument. Based on this evidence and other data, the status of the genus as an independent family,Stegnospermataceae (Stegnospermaceae) is confirmed. Apparently, it forms a connecting link betweenPhytolaccaceae andCaryophyllaceae.     

Crystallization and preliminary X-ray investigation of uridine phosphorylase from Escherichia coli

Crystals of uridine phosphorylase from Escherichia coli K12 have been grown from solutions of polyethylene glycol 4000. The crystals are trigonal, space group R3; the hexagonal axes are a = 154.4 A and c = 49.4 A. The crystals are quite stable to x-rays and diffract beyond 2.6 A resolution. It appears that the molecule is a hexamer with a subunit molecular weight of 27,500 and utilizes the 3-fold symmetry of the space group, resulting in two subunits/asymmetric unit.     

Identification of a trpG-related glutamine amide transfer domain in Escherichia coli GMP synthetase

An improved method was developed to align related protein sequences and search for homology. A glutamine amide transfer domain was identified in an NH2-terminal segment of GMP synthetase from Escherichia coli. Amino acid residues 1-198 in GMP synthetase are homologous with the glutamine amide transfer domain in trpG X D-encoded anthranilate synthase component II-anthranilate phosphoribosyltransferase and the related pabA-encoded p-aminobenzoate synthase component II. This result supports a model for gene fusion in which a trpG-related glutamine amide transfer domain was recruited to augment the function of a primitive NH3-dependent GMP synthetase. Sequence analyses emphasize that glutamine amide transfer domains are thus far found only at the NH2 terminus of fused proteins. Two rules are formulated to explain trpG and trpG-related fusions. (i) trpG and trpG-related genes must have translocated immediately up-stream of genes destined for fusion in order to position a glutamine amide transfer domain at the NH2 terminus after fusion. (ii) trpG and trpG-related genes could not translocate adjacent to a regulatory region at the 5' end of an operon. These rules explain known trpG-like fusions and explain why trpG and pabA are not fused to trpE and pabB, respectively. Alignment searches of GMP synthetase with two other enzymes that bind GMP, E. coli amidophosphoribosyltransferase and human hypoxanthine-guanine phosphoribosyltransferase, suggest a structurally homologous segment which may constitute a GMP binding site.     

Molecular dynamic simulations and structure-based pharmacophore development for farnesyltransferase inhibitors discovery

Farnesyltransferase is one of the enzyme targets for the development of drugs for diseases, including cancer, malaria, progeria, etc. In the present study, the structure-based pharmacophore models have been developed from five complex structures (1LD7, 1NI1, 2IEJ, 2ZIR and 2ZIS) obtained from the protein data bank. Initially, molecular dynamic (MD) simulations were performed for the complexes for 10?ns using AMBER 12 software. The conformers of the complexes (75) generated from the equilibrated protein were undergone protein–ligand interaction fingerprint (PLIF) analysis. The results showed that some important residues, such as LeuB96, TrpB102, TrpB106, ArgB202, TyrB300, AspB359 and TyrB361, are predominantly present in most of the complexes for interactions. These residues form side chain acceptor and surface (hydrophobic or π–π) kind of interactions with the ligands present in the complexes. The structure-based pharmacophore models were generated from the fingerprint bits obtained from PLIF analysis. The pharmacophore models have 3–4 pharmacophore contours consist of acceptor and metal ligation (Acc & ML), hydrophobic (HydA) and extended acceptor (Acc2) features with the radius ranging between 1–3?Å for Acc & ML and 1–2?Å for HydA. The excluded volumes of the pharmacophore contours radius are between 1–2?Å. Further, the distance between the interacting groups, root mean square deviation (RMSD), root mean square fluctuation (RMSF) and radial distribution function (RDF) analysis were performed for the MD-simulated proteins using PTRAJ module. The generated pharmacophore models were used to screen a set of natural compounds and database compounds to select significant HITs. We conclude that the developed pharmacophore model can be a significant model for the identification of HITs as FTase inhibitors.     

Utilization of in silico EST–SSR markers for diversity studies in castor (<Emphasis Type="Italic">Ricinus communis</Emphasis> L.)

Castor (Ricinus communis L.) a chief non-edible oilseed crop has numerous industrial applications. Systematic genetic diversity analysis utilizing DNA based markers has been quick and reliable method that ensures selection of diverse parents for exploitation of higher levels of heterosis in breeding programs. From NCBI database, 63,852 EST sequences of castor were mined. One thousand one hundred and five (1105) EST–SSRs and 1652 repeat motifs sequences were identified from 20,495 non-redundant unigene sequences. Repeat motifs consisted of 29.7 % mono nucleotide repeats, 24.8 % di nucleotide repeats, 27.27 % tri nucleotide repeats and 3.94 % tetra nucleotide repeats. Twenty eight primer pairs were chosen from SSR-containing ESTs to determine genetic diversity among 27 castor accessions. Twelve EST–SSRs showed polymorphism. Number of alleles detected were 2–3 with an average of 2.33 per locus. 150–400 bp was the size of an allele. Dendrogram analysis grouped the 27 accessions into two separate clusters. Genetic similarity coefficient of dendrogram ranged from 0.24 to 0.83. The polymorphic information content value of 0.28–0.49 revealed medium level of diversity in castor. Results of present study indicated that EST–SSRs to be efficient markers for genetic diversity studies. Knowledge on level of diversity existing in castor genotypes would be useful for breeders to plan efficient hybrid breeding programme.     

Pectinolytic enzymes produced byAspergillus carbonarius (Bainier) thom

Summary Aspergillus carbonarius produces exocellular pectinolytic enzymes which are active within the acid range of pH and therefore are useful in commercial processing of fruits. The fungus produces pectin methylesterase, a viscosity-reducing enzyme, and exo-polygalacturonase; but it does not produce transeliminases. The optimum pH range and temperature for the above-mentioned enzyme activities are 3.5 to 4.0 and 50°, respectively. Enzymic hydrolysates of both pectin and pectic acid contained only monogalacturonate. The enzymes are stable at pH 3.0 to 4.5 at room temperature (20–30°) for more than a month. A preliminary purification yielded two fractions, both of which showed viscosity-reducing as well as saccharogenic activities. Pectin methylesterase was unaffected when treated with 6M urea for 5 hr at pH 6.7 and 25°, whereas polygalacturonase and viscosityreducing activities were completely inactivated.     

Seed germinability and longevity influences regeneration of <Emphasis Type="Italic">Acacia gerrardii</Emphasis>

Acacia gerrardii is the only native tree species of the Kuwaiti desert ecosystem. However, anthropogenic disturbances and harsh arid climate have contributed towards the disappearance of this keystone species from its habitat. In this study, effects of different seed pretreatments to break dormancy, water entry pathway, and ecology (seasonal timing) of dormancy loss and germination of A. gerrardii were investigated. Effects of mechanical scarification, hot water treatment (30 s, 1, 2, and 5 min), and concentrated acid scarification (10, 20, and 30 min) on germination percentage and rate (time to 50% germination and final germination) were also examined. Pretreatment with mechanical scarification produced the highest germination in the least time and 20 °C, 40% RH with 12 h of light (2370 Lux) were found to provide the best germination environment. Seeds were rapidly aged at 60% RH and 45 or 50 °C to determine longevity, and the results were analyzed using probit analysis. Times taken for viability of A. gerrardii seeds aged at 45 and 50 °C to fall to 50% (p₅₀) were 38.6 and 9.3 days, respectively, and therefore the seeds can be considered to have medium longevity. Experiments to find the water entry pathway in A. gerrardii indicated that the micropyle region was the primary point of water entry into the seed. Seed burial experiments indicated that though seed retention decreased over time, there was no significant decrease in number of viable seeds after 31 weeks. The findings of this study are important to nursery managers, seed banks, and those involved in conservation and restoration activities.