Metal-ion-mediated tuning of duplex DNA binding by bis(2-(2-pyridyl)-1H-benzimidazole)

Studies of double-stranded-DNA binding have been performed with three isomeric bis)2-(n-pyridyl)-1H-benzimidazole)s (n = 2, 3, 4). Like the well-known Hoechst 33258, which is a bisbenzimidazole compound, these three isomers bind to the minor groove of duplex DNA. DNA binding by the three isomers was investigated in the presence of the divalent metal ions Mg2+, Co2+, Ni2+, Cu2+, and Zn2+. Ligand-DNA interactions were probed with fluorscence and circular dichroism spectroscopy. These studies revealed that the binding of the 2-pyridyl derivative to DNA is dramatically reduced in the presence of Co2+, Ni2+, and Cu2+ ions and is abolished completely at a ligand/metal-cation ratio of 1:1. Control experiments done with the isomeric 3- and 4-pyridyl derivatives showed that their binding to DNA is unaffected by the aforementioned transition-metal ions. The ability of 2-(2-pyridyl)benzimidazole changes of the ligand associated with ion chelation probably ledto such unusual binding results for the ortho isomer. The addition of ethylenediaminetetraacetic acid (EDTA) reversed the effects completely.

A bile acid derived potassium ion sensor

A chenodeoxycholic acid based K+ ion sensor has been designed using a modular approach in which a fluorophore and a cation receptor are attached to the bile acid backbone. In the absence of K+ the fluorescence of the molecule is quenched because of through-space, photo-induced electron-transfer from the aza-crown unit. Fluorescence enhancement was observed upon titration with K+ (and other alkali metal ions too). In methanol, good selectivity towards the sensing of K+ has been observed.

Zervamicins, a structurally characterised peptide model for membrane ion channels

Voltage dependent membrane channels are formed by the zervamicins, a group of α-aminoisobutyric acid containing peptides. The role of polar residues like Thr, Gln and Hyp in promoting helical bundle formation is established by dramatically reduced channel lifetimes for a synthetic apolar analog. Crystal structures of Leu1-zervamicin reveal association of bent helices. Polar contacts between convex faces result in an ‘hour glass’ like arrangement of an aqueous channel with a central constriction. The structure suggests that gating mechanisms may involve movement of the Gln11 carboxamide group. Gln3 may play a role in modulating the size of the channel mouth.

Ion channel formation by zervamicin-IIB. A molecular modelling study.

Zervamicin-IIB (Zrv-IIB) is a 16 residue peptaibol which forms voltage-activated, multiple conductance level channels in planar lipid bilayers. A molecular model of Zrv-IIB channels is presented. The structure of monomeric Zrv-IIB is based upon the crystal structure of Zervamicin-Leu. The helical backbone is kinked by a hydroxyproline residue at position 10. Zrv-IIB channels are modelled as helix bundles of from 4 to 8 parallel helices surrounding a central pore. The monomers are packed with their C-terminal helical segments in close contact, and the bundles are stabilized by hydrogen bonds between glutamine 11 and hydroxyproline 10 of adjacent helices. Interaction energy profiles for movement of three different probes species (K+, Cl- and water) through the central pore are analyzed. The conformations of: (a) the sidechain of glutamine 3; (b) the hydroxyl group of hydroxyproline 10; and (c) the C-terminal hydroxyl group are "optimized" in order to maximize favourable interactions between the channel and the probes, resulting in favourable interaction energy profiles for all three. This suggests that conformational flexibility of polar sidechains enables the channel lining to mimic an aqueous environment.

Conformation of the flexible bent helix of Leu1-zervamicin in crystal C and a possible gating action for ion passage

The membrane channel-forming polypeptide, Leu(1)-zervamicin, Ac-Leu-Ile-Gln-Iva-Ile(5)-Thr-Aib-Leu-Aib-Hyp(10) -Gln-Aib-Hyp-Aib-Pro(15)-Phol (Aib: alpha-aminoisobutyric acid; Iva: isovaline; Hyp: 4-hydroxyproline; Phol: phenylalininol) has been analyzed by x-ray diffraction in a third crystal form. Although the bent helix is quite similar to the conformations found in crystals A and B, the amount of bending is more severe with a bending angle approximate to 47 degrees, The water channel formed by the convex polar faces of neighboring helices is larger at the mouth than in crystals A and B, and the water sites have become disordered. The channel is interrupted in the middle by a hydrogen bond between the OH of Hyp(10) and the NH2 of the Gln(11) of a neighboring molecule. The side chain of Gln(11) is wrapped around the helix backbone in an unusual fashion in order that it can augment the polar side of the helix. In the present crystal C there appears to be an additional conformation for the Gln(11) side chain (with approximate to 20% occupancy) that opens the channel for possible ion passage. Structure parameters for C85H140N18O22.xH(2)O.C2H5OH are space group P2(1)2(1)2(1), a = 10.337 (2) Angstrom, b = 28.387 (7) Angstrom, c = 39.864 (11) Angstrom, Z = 4, agreement factor R = 12.99% for 3250 data observed > 3 sigma(F), resolution = 1.2 Angstrom. (C) 1994 John Wiley & Sons, Inc.

Characterization of Alkali Induced Formation of Lanthionine, Trisulfides, and Tetrasulfides from Peptide Disulfides using Negative Ion Mass Spectrometry

Peptide disulfides are unstable under alkaline conditions, resulting in the formation of products containing lanthionine and polysulfied linkages. Electrospray ionization mass spectrometry has been used to characterize major species obtained when cyclic and acyclic peptide disulfides are exposed to alkaline media. Studies on a model cyclic peptide disulfide (Boc - Cys - Pro - Leu - Cys - NHMe) and an acyclic peptide, oxidized glutathione, bis ((gamma)Glu Cys - Gly - COOH), are described. Disulfide cleavage reactions are initiated by the abstraction of (CH)-H-alpha or (CH)-H-beta protons of Cys residues, with Subsequent elimination of H2S or H2S2. The buildup of reactive thiol species which act on intermediates containing dehydroalanine residues, rationalizes the formation of lanthionine and polysulfide products. In the case of the cyclic peptide disulfide, the formation of cyclic products is facilitated by the intramolecular nature of the Michael addition reaction of thiols to the dehydroalanine residue. Mass spectral evidence for the intermediate species is presented by using alkylation of thiol groups as a trapping method. Mass spectral fragmentation in the negative ion mode of the peptides derived from trisulfides and tetrasulfides results in elimination of S-2. (J Am Soc Mass Spectrom 2009, 20, 783-791) (C) 2009 American Society for Mass Spectrometry.

Characterization of Alkali Induced Formation of Lanthionine, Trisulfides, and Tetrasulfides from Peptide Disulfides using Negative Ion Mass Spectrometry

Peptide disulfides are unstable under alkaline conditions, resulting in the formation of products containing lanthionine and polysulfied linkages. Electrospray ionization mass spectrometry has been used to characterize major species obtained when cyclic and acyclic peptide disulfides are exposed to alkaline media. Studies on a model cyclic peptide disulfide (Boc - Cys - Pro - Leu - Cys - NHMe) and an acyclic peptide, oxidized glutathione, bis ((gamma)Glu Cys - Gly - COOH), are described. Disulfide cleavage reactions are initiated by the abstraction of (CH)-H-alpha or (CH)-H-beta protons of Cys residues, with Subsequent elimination of H2S or H2S2. The buildup of reactive thiol species which act on intermediates containing dehydroalanine residues, rationalizes the formation of lanthionine and polysulfide products. In the case of the cyclic peptide disulfide, the formation of cyclic products is facilitated by the intramolecular nature of the Michael addition reaction of thiols to the dehydroalanine residue. Mass spectral evidence for the intermediate species is presented by using alkylation of thiol groups as a trapping method. Mass spectral fragmentation in the negative ion mode of the peptides derived from trisulfides and tetrasulfides results in elimination of S-2. (J Am Soc Mass Spectrom 2009, 20, 783-791) (C) 2009 American Society for Mass Spectrometry.

Hall thruster sequencer using Intel-8051 microcontroller for ion thrust measurement

Hall thrusters, such as Stationary Plasma Thruster (SPT), have been widely used on board modern satellites placed in geo-synchronows orbits for reasons such as orbit maintenance, repositioning and attitude control. In order to study the performance of the stationary plasma thruster, the thrust produced by it has been measured, using a thrust balance with strain gauge sensors under vacuum conditions, by activating the thruster. This activation of thruster has been carried out by switching ON and switching OFF of the necessary power supplies and control of other feed system such as the propellant flow in a particular sequence. Hitherto, these operations were done manually in the required sequence. This paper reports the attempt made to automate the sequential operation of the power supplies and the necessary control valves of the feed system using Intel 8051 microcontroller. This automation has made thrust measurements easier and more sophisticated.

Preparation of lithium amalgam

Lithium amalgam is useful in effecting Wurtz type intramolecular and intermolecular coupling reactions.

Crystal co-ordination of the barium ion

A systematic study has been made of the crystal co-ordination of the barium ion in various compounds whose structures have been solved. Apart from the more common co-ordination polyhedra which are enumerated in text-books, a number of new polyhedra have been identified, particularly in cases where the co-ordination numbers are unusual, such as ten or eleven. According to the radius-ratio rule of Pauling, a co-ordination number of nine or ten is normally expected for the barium ion. The present investigations, however, reveal that it shows a variety of co-ordinations with ligancies from six up to twelve. Some of the factors that might possibly enter in explaining this wide range of co-ordination numbers are discussed. It appears as though the part played by the Ba2+ ion in deciding the structure is secondary, limiting itself only to occupying vacant spaces provided by other atoms in the crystal.

Reaction of carbon disulfide with azide ion

Carbon disulfide reacts with azide ion to form the 1,2,3,4-thiatriazolinethionate ion and not the acyclic azido dithiocarbonate ion as previously reported. A series of salts of thiatriazoline have been prepared and none shows evidence for the presence of the azido group. Esters of thiatriazolinethione prepared by the reaction of the sodium salt with alkyl or acyl halides have been found to be either 5-(substituted) mercapto-1,2,3,4-thiatriazoles or 4-substituted 1,2,3,4-thiatriazoline-5-thiones. These structures have been assigned on the basis of degradative and spectroscopic evidence. The chemistry of the so-called azidodithiocarbonates has been reinterpreted in terms of the thiatriazole structure.

Dispenser ion emitters

The development of a dispenser type of ion emitter is described. This type of ion emitter has been used successfully for obtaining lead, aluminum, and tin ions.

Steroids and related natural products. VII. Boron trifluoride etherate-lithium aluminum hydride reduction of smilagenin acetate

Reduction of smilagenin acetate (Va) using a boron trifluoride etherate-lithium aluminum hydride reagent, followed by hydrogen peroxide oxidation and acetylation, was found to yield: 3β-ethoxysmilagenin (Vb), 3β-ethoxydihydrosmilagenin acetate (VIa), dihydrosmilagenin diacetate (VIb), and a complex mixture of partially acetylated products. Similar reaction conditions were employed to convert dihydrodiosgenin (II) to dihydrochlorogenin (III). Boron trifluoride etherate-lithium aluminum hydride reduction of 3β-acetoxy-5α-cholestane and 3β-acetoxy-5α-lanostane (VIIIa) was shown to yield the corresponding 3β-ethoxy (e.g., VIIIb) derivatives.