Characterization of alpha helices interacting with nucleic acids

Protein-nucleic acid interactions play a vital role in most genetic processes. An enhanced insight into such interactions can be obtained from the structure database of these complexes. Here, we report an overall survey on the geometry of alpha helices which interact with nucleic acids through hydrogen bonds and/or non-bonded interactions. Using the program RADIL based on an algorithm developed from this laboratory, 161 alpha helices in 70 non-redundant nucleic acid binding protein chains solved using X-ray crystallography are analysed. The helical geometry has been characterized as bent, canonical, terminally or completely distorted. The analysis reveals that approximately 70% of the alpha helices possess distortions of any one kind, viz., bend, terminal distortion or complete distortion. Nearly one-third of the total helices possess bends, with a majority of the bending occurring in 5-15 degrees range. In addition, a majority of the bent helices approach the nucleic acid helix in a perpendicular direction. The program RADIL has been useful in characterizing the nucleic acid-induced structural variations in alpha helices, however small they may be.     

Selection of pH-related parameters in ion-exchange chromatography using pH-gradient operations

This work demonstrates that the type of ion-exchanger (anion or cation), the mode of operation (bind-and-elute or flow-through), and the operational pH of ion-exchange chromatography (IEX) can be selected in a fast and rational way by analytical pH-gradient IEX operations, thereby eliminating the need for pH scouting or high-throughput screening. The developed approach was applied for the selection of an IEX process for the capture of a monoclonal antibody (MAb) from hybridoma cell culture supernatant (CCS). It was found within a day that MAb can optimally be captured by bind-and-elute mode cation-exchange chromatography (CEX) at pH 4.5 or anion-exchange chromatography (AEX) at pH 7.2 without lowering the salt concentration in the CCS. The performance of both CEX and AEX was predicted to be equal for this particular MAb capture.     

Carboxylic acid–pyridine supramolecular heterocatemer in a co-crystal

Robustness of carboxylic acid–pyridine supramolecular heterosynthon was examined in three 1:2 binary co-crystals of 4,4′-bipyridine with monocarboxylic acids, (4,4′-bipyridine)·(dl-hydroxyphenylacetic acid)₂, 1; (4,4′-bipyridine)_0.5·(4-bromonaphthalene-1-carboxylic acid), 2 and (4,4′-bipyridine)_0.5·(4-methylbenzoic acid), 3. All the three co-crystals form “two-component supermolecules” (consisting of one molecule of 4,4′-bipyridine and two molecules of the relevant carboxylic acid) stabilized through carboxylic acid–pyridine heterosynthons. Co-crystals 1 and 2 exhibits the expected carboxylic acid–pyridine dimer (heterodimer I) whereas co-crystal 3 forms a novel carboxylic acid–pyridine catemer (heterocatemer II).     

4-Salicylideneamino-3-methyl-1,2,4-triazole-5-thione as a sensor for aniline recognition

Tridentate triazole based Schiff base 4-salicylideneamino-3-methyl-1,2,4-triazole-5-thione has been found to selectively detect toxic aromatic amines such as aniline and benzene-1,4-diamine by simple titration techniques like UV-visible, fluorescence spectral studies (PL) and 1H NMR titrations. The Schiff base receptor utilizes, thione sulfur, NH-thione and the phenolic hydroxyl group to form hydrogen bonded adduct of aniline and benzene-1,4-diamine with high binding affinity, followed by a slow removal of the corresponding hydrogens thus providing a promising candidate and an unique receptor for toxic aromatic amines.     

Differentiating the gum resins of two closely related Indian Gardenia species, G. gummifera and G. lucida, and establishing the source of dikamali gum resin using high-performance thin-layer chromatography and ultra-performance liquid chromatography-UV/MS

Dikamali is a gum resin obtained from the leaf buds of Gardenia lucida or G. gummifera. There is controversy regarding the botanical source of this gum resin with some stating it to be from G. lucida while others claim it to be from G. gummifera. Analytical methods including UPLC and HPTLC were developed for the qualitative analysis of Gardenia species and various commercial samples. The separation using a UPLC method was achieved within 12.0 min by using C18 column material, a water/acetonitrile mobile phase, both containing formic acid, a gradient system, and a temperature of 40 degrees C. Extensive studies of dikamali collected from various parts of India in comparison with the gum resins collected from G. lucida and G. gummifera clearly indicated that the botanical source of commercially available dikamali is G. lucida, not G. gummifera. The marker compounds isolated from a market sample of dikamali were present only in the gum resin of G. lucida and the compounds isolated from G. gummifera were not present in any of the dikamali samples, confirming the botanical source of dikamali. This work is of utmost importance, given the ambiguity regarding the botanical source of the gum resin dikamali. LC/MS coupled with electrospray ionization is described for the identification and confirmation of nine compounds from various samples of the gum resin. An HPTLC method was also developed for the fast chemical fingerprint analysis of Gardenia samples.     

Aromatic hydrogenation over nickel-silica prepared by deposition-precipitation

Three different nickel/silica catalysts prepared by decomposition-precipitation are characterized by adsorption technique and evaluated for aromatic hydrogenation. Depending on the metal content and the available surface nickel, activity and selectivity are affected for the reactions studied.     

Bis[1‐(pyridin‐2‐yl)­ethano­ne‐κN 4‐phenyl­thio­semicarbazonato‐κ2N4,S]­manganese(II)

One half of the mol­ecule of the title complex, [Mn(C₁₄H₁₃N₄S)₂], is related to the other half by a twofold axis passing through the Mn atom. This high‐spin Mn atom is six‐coordinated, in an octahedral geometry, by the azomethine N, the pyridyl N and the thiol­ate S atom of two planar 1‐­(pyridin‐2‐yl)­ethanone N(4)‐phenyl­thio­semicarbazone lig­ands. In the crystal, the mol­ecules are interconnected by N—­H?S and C—H?N interactions, forming a three‐dimensional network.     

Stereoselective total synthesis of (+)-aspicilin

A stereoselective synthesis of (+)-aspicilin is described. Regio- and stereoselective functionalization by intramolecular participation of the sulfinyl group, ene reaction, and macrolactonization by Wadsworth-Emmons reaction employing Masamune-Roush protocol are the key steps of the route.     

Silibinin is a potent sensitizer of UVA radiation-induced oxidative stress and apoptosis in human keratinocyte HaCaT cells

UVA radiation (315-400 nm), which constitutes ca 95% of the UV irradiation in natural sunlight reaching earth surface, is a major environmental risk factor associated with human skin cancer pathogenesis. UVA is an oxidizing agent that causes significant damage to cellular components through the release of reactive oxygen species (ROS) and leads to photoaging and photocarcinogenesis. Here we investigate the effect of silibinin, the flavonolignan from Silybum marianum, on UVA-induced ROS and cell death in human keratinocyte cell line HaCaT. In addition, the effect of silibinin on UVA-induced intracellular ROS-mediated endoplasmic reticulum (ER) stress was also analyzed. UVA irradiation resulted in ROS production and apoptosis in HaCaT cells in a dose-dependent manner, and the ROS levels and apoptotic index were found to be elevated significantly when the cells were treated with 75 μmsilibinin for 2 h before UVA exposure. When the cells were pretreated with 10 mmN-acetyl cysteine, the enhancement of UVA-induced apoptosis by silibinin was compromised. Furthermore, we found that silibinin enhances ER stress-mediated apoptosis in HaCaT cells by increasing the expression of CHOP protein. These results suggest that silibinin may be beneficial in the removal of UVA-damaged cells and the prevention of skin cancer.