Geochemistry of fluoride rich groundwater in Kolar and Tumkur Districts of Karnataka

Groundwater is a significant water resource in India for domestic, irrigation, and industrial needs. By far the most serious natural groundwater-quality problem in India, in terms of public health, derives from high fluoride, arsenic, and iron concentrations. Hydrogeochemical investigation of fluoride contaminated groundwater samples from Kolar and Tumkur Districts in Karnataka are undertaken to understand the quality and potability of groundwater from the study area, the level of fluoride contamination, the origin and geochemical mechanisms driving the fluoride enrichment. Majority of the groundwater samples did not meet the potable water criteria as they contained excess (>1.5 mg/L) fluoride, dissolved salts (>500 mg/L) and total hardness (75-924 mg/L). Hydrogeochemical facies of the groundwater samples suggest that rock weathering and evaporation-crystallization control the groundwater composition in the study area with 50-67% of samples belonging to the Ca-HCO3 type and the remaining falling into the mixed Ca-Na-HCO3 or Ca-Mg-Cl type. The saturation index values indicated that the groundwater in the study area is oversaturated with respect to calcite and under-saturated with respect to fluorite. The deficiency of calcium ion concentration in the groundwater from calcite precipitation favors fluorite dissolution leading to excess fluoride concentration.

Structural studies of model peptides containing beta-, gamma- and delta-amino acids

The crystal structures of five model peptides Piv-Pro-Gly-NHMe (1), Piv-Pro-beta Gly-NHMe (2), Piv-Pro-beta Gly-OMe (3), Piv-Pro-delta Ava-OMe (4) and Boc-Pro-gamma Abu-OH (5) are described (Piv:pivaloyl; NHMe: N-methylamide; beta Gly:beta-glycine; OMe:O-methyl ester; delta Ava:delta-aminovaleric acid; gamma Abu:gamma-aminobutyric acid). A comparison of the structures of peptides 1 and 2 illustrates the dramatic consequences upon backbone homologation in short sequences. 1 adopts a type II beta-turn conformation in the solid state, while in 2, the molecule adopts an open conformation with the beta-residue being fully extended. Piv-Pro-beta Gly-OMe (3), which differs from 2 by replacement of the C-terminal NH group by an O-atom, adopts an almost identical molecular conformation and packing arrangement in the solid state. In peptide 4, the observed conformation resembles that determined for 2 and 3, with the delta Ava residue being fully extended. In peptide 5, the molecule undergoes a chain reversal, revealing a beta-turn mimetic structure stabilized by a C-H center dot center dot center dot O hydrogen bond.

Conformations of peptides containing Z-alpha,beta-dehydroleucine (delta ZLeu). A comparison of Boc-Pro-delta ZLeu-Gly-NHEt and Boc-Pro-delta ZPhe-Gly-NHEt.

Two tripeptides of the type Boc-Pro-ΔZX-Gly-NHEt (where X = Leu, Phe) have been synthesized and their solution conformations investigated by 270 MHz 1H n.m.r. and i.r. spectroscopy. These conformational studies indicated that ΔZLeu, similar to ΔZPhe, has a strong tendency to stabilize folded Type II β-turn conformations when present at i + 2 position.

cAMP-regulated Protein Lysine Acetylases in Mycobacteria

Cyclic AMP synthesized by Mycobacterium tuberculosis has been shown to play a role in pathogenesis. However, the high levels of intracellularcAMP found in both pathogenic and nonpathogenic mycobacteria suggest that additional and important biological processes are regulated by characterization of novel cAMP-binding proteins in M. smegmatis and M. tuberculosis (MSMEG_5458 and Rv0998, respectively) that contain a cyclic nucleotide binding domain fused to a domain that shows similarity to the GNAT family of acetyltransferases. We detect protein lysine acetylation in mycobacteria and identify a universal stress protein (USP) as a substrate of MSMEG_5458. Acetylation of a lysine residue in USP is regulated by cAMP, and using a strain deleted for MSMEG_5458, we show that USP is indeed an in vivo substrate for MSMEG_5458. The Rv0998 protein shows a strict cAMP-dependent acetylation of USP, despite a lower affinity for cAMP than MSMEG_5458. Thus, this report not only represents the first demonstration of protein lysine acetylation in mycobacteria but also describes a unique functional interplay between a cyclic nucleotide binding domain and a protein acetyltransferase.

Conformations of dehydrophenylalanine containing peptides: nmr studies of an acyclic hexapeptide with two delta Z-Phe residues

The conformation of an acyclic dehydrophenylalanine (delta Z-Phe) containing hexapeptide, Boc-Phe-delta Z-Phe-Val-Phe-delta Z-Phe-Val-OMe, has been investigated in CDCl3 and (CD3)2SO by 270-MHz 1H-nmr. Studies of NH group solvent accessibility and observation of interresidue nuclear Overhauser effects (NOEs) suggest a significant solvent-dependent conformational variability. In CDCl3, a population of folded helical conformations is supported by the inaccessibility to solvent of the NH groups of residues 3-6 and the detection of several NiH----Ni + 1H NOEs. Evidence is also obtained for conformational heterogeneity from the detection of some Ci alpha H----Ni + 1H NOEs characteristic of extended strands. In (CD3)2SO, the peptide largely favors an extended conformation, characterized by five solvent-exposed NH groups and successive Ci alpha H----Ni + 1H NOEs for the L-residues and Ci beta H----Ni + 1H NOEs for the delta Z-Phe residues. The results suggest that delta Z-Phe residues do not provide compelling conformational constraints.

Analysis of short interproton distances in proline peptides as a guide in the interpretation of nuclear overhauser effects

The conformational dependence of interproton distances in model proline peptides has been investigated in order to facilitate interpretation of the results of Nuclear Overhauser Effect (NOE) studies on such peptides. For this purpose two model systems, namely, Ac-Pro-NHMe and Ac-Pro-X-NHMe have been chosen and used. In the former, short interproton distances detectable in NOE experiments permit a clear distinction between conformations with Pro ψ = -300 (helical region) and those in which ψ is around 1200 (polyproline region). For the latter, the variation of distances between the protons of methyl amide and the Pro ring have been studied by superimposing on the Ramachandran map in the (φ3, ψ3) plane. The results show that β-turns and non-β-turn conformations can be readily distinguished from NOE data and such long range NOEs should be detectable for specific non-β-turn conformations. NOEs involving Cβ and Cγ protons are particularly sensitive to the state of pyrrolidine ring puckering.

Stabilization of unusual structures in peptides using alpha,beta-dehydrophenylalanine: Crystal and solution structures of Boc-Pro-Delta Phe-Val-Delta Phe-Ala-OMe and Boc-Pro-Delta Phe-Gly-Delta Phe-Ala-OMe

The structures of two dehydropentapeptides, Boc-Pro-Delta Phe-Val-Delta Phe-Ala-OMe (I) and Boc-Pro-Delta Phe-Gly-Delta Phe-Ala-OMe (II) (Boc: t-butoxycarbonyl), have been determined by nuclear magnentic resonance (NMR), circular dichroism (CD), and X-ray, crystallographic studies. The peptide I assumes a S-shaped flat beta-bend structure, characterized by two partially overlapping type II beta-bends and absence of a second 1 <- 4 (N4-H center dot center dot center dot O1') intramolecular hydrogen bond. This is in contrast to the generally observed 3(10)-helical conformation in peptides with Delta Phe at alternate positions. This report describes the novel conformation assumed by peptide I and compares it with that of the conserved tip of the V3 loop of the HIV-1 envelope glycoprotein gp120 (sequence, G:P319 to F:P324, PDB code IACY). The tip of the V3 loop also assumes a S-shaped conformation with Arg:P322, making an intramolecular side-chain-backbone interaction with the carbonyl oxygen of Gly:P319. Interestingly, in peptide I, C(gamma)HVal(3) makes a similar side-chain-backbone C-H center dot center dot center dot O hydrogen bond with the carbonyl oxygen of the Boc group. The observed overall similarity indicates the possible use of the peptide as a viral antagonist or synthetic antigen. Peptide 11 adopts a unique turn followed by a 3(10)-helix. Both peptides I and II are classical examples of stabilization of unusual structures in oligopeptides.

Photochemistry of .alpha.,.beta.-unsaturated thiones: addition to electron-rich olefins from T1

1,1,3-Trimethyl-2-thioxo-1,2-dihydronaphthale(1n)e adds to electron-rich olefins upon excitation to either Sz (PP*) or Sl (ns*) states. Excitation to S2 level resulted in the same mixture of products, namely thietane and 1,4-dithiane, as on excitation to S1 level. Addition occurs to the thiocarbonyl function and not to the carbon-carbon double bond. The addition is site-specific, and the formation of thietane is regiospecific. The ratio of thietane to 1,4-dithiane in the product mixture is dependent on the concentration of the thioenone. The addition is suggested to originate from the lowest triplet state (Tl) and involves diradical intermediates.

Mechanism of interaction of the antileukemic drug cytosine arabinoside with aromatic peptides : role of sugar conformation and peptide backbone

Interaction of the antileukemic drugs, cytosine-arabinoside (Ara-C) and adenosine-arabinoside (Ara-A) and a structural analogue, cytidine, with aromatic dipeptides has been studied by fluorescence and NMR spectroscopy. Ara-C and cytidine bind tryptophanyl and histidyl dipeptides but not tyrosyl dipeptides, while Ara-A does not bind to any of them. Both studies indicate association involving stacking of aromatic moieties. NMR spectra also indicate a protonation of the histidine moiety by Ara-C. In case of cytidine, the chemical shifts observed on binding to His-Phe imply that the backbone protons of the dipeptide participate in the binding. The conformation of the sugar and the base seem to play a very important role in the binding phenomenon as three similar molecules, Ara-C, Ara-A and cytidine bind in totally different ways.

Synthetic and conformational studies on dehydrophenylalanine containing model peptides

Four model dipeptides containing a Z-dehydrophenylalanine residue (ΔZPhe) at the C-terminal, Boc-X-ΔZ Phe-NHMe (X = Ala (1), Gly (2), Pro (3), and Val (4)), have been synthesised and their solution conformations investigated by 270 MHz 1H n.m.r. and i.r. spectroscopy. N.m.r. studies on these peptides clearly show the presence of intramolecularly hydrogen bonded structures in CHCl3 solutions while such structures appear to be absent in the corresponding saturated peptides. This conclusion is also supported by i.r. studies. Studies of the nuclear Overhauser effect provided evidence for the occurrence of a significant population of β-turn structures in solvents like CDCl3 and (CD3)2SO. The observed NOES are consistent with a major contribution from Type II β-turn structure in CDCl3, while in (CD3)2SO solutions there is evidence of a partially extended structure also.

An infrared spectroscopic study of C7 intramolecular hydrogen bonds in peptides

The ir-spectra in the N-H stretching region of Piv-Pro-NHMe and Boc-Pro-NHMe have been studied in carbon tetrachloride and chloroform solutions over a wide range of concentrations. Based on the concentration dependence of the N-H stretching bands, it has been shown that the characteristic N-H stretching band due to the C7 intramolecular hydrogen bond is around 3335 cm-'. Intermolecular hydrogen bonding also occurs to a small extent in these peptides, giving rise to a slight concentration dependence of the N-H stretching bands. The band around 3335 cm-* need not necessarily be due to C7 hydrogen bonds alone as proposed by Tsuboi et al. or to intermolecular hydrogen bonding alone as proposed by Maxfield et al.; this conclusion is supported by studies on Boc-Leu-NHMe, which undergoes only intermolecular hydrogen bonding We have shown that 2-Aib-Aib-OMe and Z-Aib- Ala-OMe form C7 intramolecular hydrogen bonds in addition to C5 intramolecular hydrogen bonds. The present studies also show that all the peptides studied exist in more than one conformation in solution.

The stereochemistry of a-aminoisobutyric acid containing peptides

a-Aminoisobutyric acid (Aib), * a nonprotein amino acid first described synthetically, I has been found in diverse sources, ranging from peptides of microbial origin2s3 to the Murchison mete~r i te.E~a rly studies of the chemistry of Aib were directed towards the synthesis of model peptides containing this "sterically hindered" amino There have been several reports on the synthesis of Aib containing analogs of biologically active peptides.

Stereochemistry of peptides containing 1-aminocyclopentane carboxylic acid (Acc5). Solution and solid state conformations of Boc-Acc5-Acc5-NHMe.

The conformational analysis of a protected homodipeptide of 1-aminocyclopentanecarboxylic acid (Acc5) has been carried out. 1H-nmr studies establish a ?-turn conformation for Boc-Acc5-Acc5-NHMe in chloroform and dimethylsulfoxide solutions involving the methylamide NH in an intramolecular hydrogen bond. Supportive evidence for the formation of an intramolecular hydrogen bond is obtained from ir studies. X-ray diffraction studies reveal a type III ?-turn conformation in the solid state stabilized by a 4 ? 1 hydrogen bond between the Boc CO and methylamide NH groups. The ?,? values for both Acc5 residues are close to those expected for an ideal 310-helical conformation (?? ± 60°, ?? ±30°).