Enzymatic separation of cis and trans isomers of alicyclic alcohols

It has been discovered that phosphatases [alkaline phosphatase, orthophosphoric-monoester phosphohydrolase (alkaline optimum), EC 3.1.3.1, and acid phosphatase, orthophosphoric-monoester phosphohydrolase (acid optimum), EC 3.1.3.2] display a remarkable geometric specificity in the hydrolysis of cis and trans isomers of monoorthophosphate esters of substituted alicy clicalcohols. While steric hindrances prevent potato acid phosphatase from hydrolysing cis-2-methylcyclohexyl and cis-2-methylcyclopentyl phosphates, the corresponding trans isomers are readily hydrolysed by the enzyme (non-enzymatic, acid-catalysed or base-catalysed hydrolyses of the cis and trans isomers occur at similar rates). Cis isomers of methylcyclohexyl phosphates, in which the methyl group is remote from the hydrolysed ester bond, 3- or 4-, have nearly the same reactivities to phosphatases as their trans counterparts. However, if the methyl group in position 4 is replaced by a bulky substituent, e.g. tert-butyl, phosphatases again hydrolyse only the trans and not the cis isomer. These phenomena afford a simple method for preparative separation of cis and trans isomers of alicyclic alcohols: a mixture of the isomers is first phosphorylated with POCl₃ and then hydrolysed by phosphatase. The trans alcohol formed is extracted with CCl₄, followed by alkaline hydrolysis of the remaining cis-tester and subsequent extraction of the cis alcohol produced.     

The role of glycine (residue 89) in the central helix of EF-hand protein troponin-C exposed following amino-terminal alpha-helix deletion.

Because an N-terminal alpha-helical (N-helix) arm and a KGK-triplet (residues 88KGK90) in the central helix of troponin-C (TnC) are missing in calmodulin, several recent studies have attempted to elucidate the structure-function correlations of these units. Presently, with a family of genetically manipulated derivatives especially developed for this study and tested on permeabilized isolated single skeletal muscle fiber segments, we explored the specificities of the amino acid residues within the N-helix and the KGK-triplet in TnC. Noticeably, the amino acid compositions vary between the N-helices of the cardiac and skeletal TnC isoforms. On the other hand, the KGK-triplet is located similarly in both TnC isoforms. We previously indicated that deletion of the N-helix (mutant delta Nt) diminishes the tension obtained on activation with maximal calcium, but the contractile function is revived by the superimposed deletion of the 88KGK90-triplet (mutant delta Nt delta KGK; see Gulati J, Babu A, Su H, Zhang YF, 1993, J Biol Chem 268:11685-11690). Using this functional test, we find that replacement of Gly-89 with a Leu or an Ala could also overcome the contractile defect associated with N-helix deletion. On the other hand, replacement of the skeletal TnC N-helix with cardiac type N-helix was unable to restore contractile function. The findings indicate a destabilizing influence of Gly-89 residue in skeletal TnC and suggest that the N-terminal arm in normal TnC serves to moderate this effect. Moreover, specificity of the N-helix between cardiac and skeletal TnCs raises the possibility that resultant structural disparities are also important for the functional distinctions of the TnC isoforms.     

A pathway map of glutamate metabolism

Glutamate metabolism plays a vital role in biosynthesis of nucleic acids and proteins. It is also associated with a number of different stress responses. Deficiency of enzymes involved in glutamate metabolism is associated with various disorders including gyrate atrophy, hyperammonemia, hemolytic anemia, γ-hydoxybutyric aciduria and 5-oxoprolinuria. Here, we present a pathway map of glutamate metabolism representing metabolic intermediates in the pathway, 107 regulator molecules, 9 interactors and 3 types of post-translational modifications. This pathway map provides detailed information about enzyme regulation, protein-enzyme interactions, post-translational modifications of enzymes and disorders due to enzyme deficiency. The information included in the map was based on published experimental evidence reported from mammalian systems.     

Novel reactivity aspects of cis-bis(1-alkenyl)platinum(II) compounds of the type Pt(CH2(CH2)nCHCH2)2L2 (where L2 = dppp, dppe, dppm and n = 1, 2)

We describe the synthesis, structure and reactivity of novel bis(1-alkenyl)platinum(II) complexes, Pt[CH₂(CH₂)_nCHCH₂]₂L₂ (where L₂ = dppp, dppe, dppm and n = 1, 2). The stability of the title complexes with the different ligands is discussed. The steric, chelating and electronic properties of the ligands have a significant impact on the structure as well as on the reactivity of the complexes. Novel reactions with elemental sulfur and carbon dioxide are described and discussed.     

Determinants that control the specific interactions between TAB1 and p38alpha

Previous studies have revealed that transforming growth factor-beta-activated protein kinase 1 (TAB1) interacts with p38alpha and induces p38alpha autophosphorylation. Here, we examine the sequence requirements in TAB1 and p38alpha that drive their interaction. Deletion and point mutations in TAB1 reveal that a proline residue in the C terminus of TAB1 (Pro412) is necessary for its interaction with p38alpha. Furthermore, a cryptic D-domain-like docking site was identified adjacent to the N terminus of Pro412, putting Pro412 in the phi(B)+3 position of the docking site. Through mutational analysis, we found that the previously identified hydrophobic docking groove in p38alpha is involved in this interaction, whereas the CD domain and ED domain are not. Furthermore, chimeric analysis with p38beta (which does not bind to TAB1) revealed a previously unidentified locus of p38alpha comprising Thr218 and Ile275 that is essential for specific binding of p38alpha to TAB1. Converting either of these residues to the corresponding amino acid of p38beta abolishes p38alpha interaction with TAB1. These p38alpha mutants still can be fully activated by p38alpha upstream activating kinase mitogen-activated protein kinase kinase 6, but their basal activity and activation in response to some extracellular stimuli are reduced. Adjacent to Thr218 and Ile275 is a site where large conformational changes occur in the presence of docking-site peptides derived from p38alpha substrates and activators. This suggests that TAB1-induced autophosphorylation of p38alpha results from conformational changes that are similar but unique to those seen in p38alpha interactions with its substrates and activating kinases.     

Mapping the NPHP-JBTS-MKS protein network reveals ciliopathy disease genes and pathways

Nephronophthisis (NPHP), Joubert (JBTS), and Meckel-Gruber (MKS) syndromes are autosomal-recessive ciliopathies presenting with cystic kidneys, retinal degeneration, and cerebellar/neural tube malformation. Whether defects in kidney, retinal, or neural disease primarily involve ciliary, Hedgehog, or cell polarity pathways remains unclear. Using high-confidence proteomics, we identified 850 interactors copurifying with nine NPHP/JBTS/MKS proteins and discovered three connected modules: "NPHP1-4-8" functioning at the apical surface, "NPHP5-6" at centrosomes, and "MKS" linked to Hedgehog signaling. Assays for ciliogenesis and epithelial morphogenesis in 3D renal cultures link renal cystic disease to apical organization defects, whereas ciliary and Hedgehog pathway defects lead to retinal or neural deficits. Using 38 interactors as candidates, linkage and sequencing analysis of 250 patients identified ATXN10 and TCTN2 as new NPHP-JBTS genes, and our Tctn2 mouse knockout shows neural tube and Hedgehog signaling defects. Our study further illustrates the power of linking proteomic networks and human genetics to uncover critical disease pathways.     

Adaptive developmental plasticity in methylene tetrahydrofolate reductase (MTHFR) C677T polymorphism limits its frequency in South Indians

Methylene tetrahydrofolate reductase (MTHFR) C677T polymorphism shows considerable heterogeneity in its distribution in humans worldwide. The current study was conducted to investigate whether this polymorphism exhibited adaptive developmental plasticity in the control of the TT-genotype frequency. We screened 1,818 South Indian subjects (895 males and 923 females) for MTHFR C677T polymorphism using PCR–restriction fragment length polymorphism approach. MTHFR 677T-allele frequency in males and females was 9.1 and 11.0 %, respectively. Compared to females, males had lower frequency of TT-genotype [odds ratio 0.31, 95 % confidence interval (CI) 0.08–1.01]. The frequency of MTHFR 677T-allele was highest in the age group of 20–40 years and it gradually decreased from 40–60 to 60–80 years (P _trend <0.0001). MTHFR 677TT-genotype was associated with 7.02-folds (95 % CI: 2.12–25.63, P < 0.0001) cumulative risk for recurrent pregnancy loss (RPL), neural tube defects (NTDs) and deep vein thrombosis (DVT). Linear regression model suggested that male gender exhibited increased homocysteine levels by 9.35 μmol/L while each MTHFR 677T-allele contributed to 4.63 μmol/L increase in homocysteine. Plasma homocysteine showed inverse correlation with dietary folate (r = ?0.17, P < 0.0001), B₂ (r = ?0.14, P < 0.0001) and B₆ (r = ?0.07, P = 0.03). Examination of the spontaneously aborted fetuses (n = 35) showed no significant association of fetal genotype on its in utero viability. From the current study, it was concluded that C677T seemed to have acquired adaptive developmental plasticity among South Indians due to environmental influences thus contributing to hyperhomocysteinemia and its associated complications such as RPL, NTDs, DVT, etc.     

Identification of the Aggregation Pheromone of the Melon Thrips,Thrips palmi

The objective of this study was to identify the aggregation pheromone of the melon thrips Thrips palmi, a major pest of vegetable and ornamental plants around the world. The species causes damage both through feeding activities and as a vector of tospoviruses, and is a threat to world trade and European horticulture. Improved methods of detecting and controlling this species are needed and the identification of an aggregation pheromone will contribute to this requirement. Bioassays with a Y-tube olfactometer showed that virgin female T. palmi were attracted to the odour of live males, but not to that of live females, and that mixed-age adults of both sexes were attracted to the odour of live males, indicating the presence of a male-produced aggregation pheromone. Examination of the headspace volatiles of adult male T. palmi revealed only one compound that was not found in adult females. It was identified by comparison of its mass spectrum and chromatographic details with those of similar compounds. This compound had a structure like that of the previously identified male-produced aggregation pheromone of the western flower thrips Frankliniella occidentalis. The compound was synthesised and tested in eggplant crops infested with T. palmi in Japan. Significantly greater numbers of both males and females were attracted to traps baited with the putative aggregation pheromone compared to unbaited traps. The aggregation pheromone of T. palmi is thus identified as (R)-lavandulyl 3-methyl-3-butenoate by spectroscopic, chromatographic and behavioural analysis.     

Reduction of Nitrite and Nitrate to Ammonium on Pyrite

An important constraint on the formation of the building blocks of life in the Hadean is the availability of small, activated compounds such as ammonia (NH(3)) relative to its inert dinitrogen source. Iron-sulfur particles and/or mineral surfaces have been implicated to provide the catalytic active sites for the reduction of dinitrogen. Here we provide a combined kinetic, spectroscopic, and computational modeling study for an alternative source of ammonia from water soluble nitrogen oxide ions. The adsorption of aqueous nitrite (NO (2) (-) ) and nitrate (NO (3) (-) ) on pyrite (FeS(2)) and subsequent reduction chemistry to ammonia was investigated at 22°C, 70°C, and 120°C. Batch geochemical and in situ Attenuated Total Reflection - Fourier Transform Infrared (ATR-FTIR) spectroscopy experiments were used to determine the reduction kinetics to NH(3) and to elucidate the identity of the surface complexes, respectively, during the reaction chemistry of NO (2) (-) and NO (3) (-) . Density functional theory (DFT) calculations aided the interpretation of the vibrational data for a representative set of surface species. Under the experimental conditions used in this study, we detected the adsorption of nitric oxide (NO) intermediate on the pyrite surface. NH(3) production from NO (2) (-) occurred at 70 and 120°C and from NO (3) (-) occurred only at 120°C.     

Unique MAP Kinase binding sites

Map kinases are drug targets for autoimmune disease, cancer, and apoptosis-related diseases. Drug discovery efforts have developed MAP kinase inhibitors directed toward the ATP binding site and neighboring "DFG-out" site, both of which are targets for inhibitors of other protein kinases. On the other hand, MAP kinases have unique substrate and small molecule binding sites that could serve as inhibition sites. The substrate and processing enzyme D-motif binding site is present in all MAP kinases, and has many features of a good small molecule binding site. Further, the MAP kinase p38alpha has a binding site near its C-terminus discovered in crystallographic studies. Finally, the MAP kinases ERK2 and p38alpha have a second substrate binding site, the FXFP binding site that is exposed in active ERK2 and the D-motif peptide induced conformation of MAP kinases. Crystallographic evidence of these latter two binding sites is presented.