Proteins: sequence to structure and function--current status

In an era that has been dominated by Structural Biology for the last 30-40 years, a dramatic change of focus towards sequence analysis has spurred the advent of the genome projects and the resultant diverging sequence/structure deficit. The central challenge of Computational Structural Biology is therefore to rationalize the mass of sequence information into biochemical and biophysical knowledge and to decipher the structural, functional and evolutionary clues encoded in the language of biological sequences. In investigating the meaning of sequences, two distinct analytical themes have emerged: in the first approach, pattern recognition techniques are used to detect similarity between sequences and hence to infer related structures and functions; in the second ab initio prediction methods are used to deduce 3D structure, and ultimately to infer function, directly from the linear sequence. In this article, we attempt to provide a critical assessment of what one may and may not expect from the biological sequences and to identify major issues yet to be resolved. The presentation is organized under several subtitles like protein sequences, pattern recognition techniques, protein tertiary structure prediction, membrane protein bioinformatics, human proteome, protein-protein interactions, metabolic networks, potential drug targets based on simple sequence properties, disordered proteins, the sequence-structure relationship and chemical logic of protein sequences.     

A validated HPTLC method for determination of trans-caryophyllene from polyherbal formulations

Formulations of traditional medicines are usually made up of a complex mixture of herbs. However, effective quality control methods in order to select materials of the right quality are lacking. 'Amukkara choornam' is a polyherbal Siddha formulation used for gastritis, spleen enlargement, leucorrhoea, hiccups, anaemia, tuberculosis and kappa diseases. Trans-caryophyllene is an important constituent present in the ingredients of this formulation. In a literature survey, it was found that there is no such method for the quantification of trans-caryophyllene except gas chromatography or gas chromatography-mass spectroscopy (GC-MS). So, a high performance thin layer chromatography (HPTLC) method was developed and validated for the quantification of trans-caryophyllene in amukkara choornam. Pre-coated silica gel 60F-254 plates (10 × 10 cm2) were used for the analysis. The solvent system consisted of toluene-ethyl acetatate (9 : 3, v/v), and trans-caryophyllene was detected at 260 nm. The developed method was validated for linearity (R2 = 0.9996 ± 0.0034), limit of detection (LOD) (0.101 ng), limit of quantification (LOQ) (0.639 ng), accuracy (% recovery = 97.19 ± 1.204), and precision (CV < 5%, for both intra-day and inter-day precisions). The levels of trans-caryophyllene were found to be 3.5-4.10 μg per gram of herbal products.     

Superconductivity of Y–Ba–Cu–O and substituted systems

Superconductivity of Y-Ba-Cu-O system is studied in the composition 2:2:3 and 1:2:3 of Y:Ba:Cu. The effect of replacement of Y or Ba by divalent Sr and Ca, trivalent Ce and tetravalent Zr is studied. X-ray diffraction, SEM and TEM techniques are used for materials characterization. Superconducting transition temperatures are measured resistively. Rapid resistance drop observed above 230 K in Y-Ba-Sr-Cu-O and Y-Ba-Ca-Cu-O systems indicate the possible existence of superconductivity above 230 K. Substitution of Ce in place of Y is found to reduce the onset Tc from 95 K to 80 K. For the first time, replacement of Cu by Zr in Y-Ba-Cu-O has yielded the onset Tc of about 105 K.     

Effect of quaternary ammonium cations on dye sorption to fly ash from aqueous media

The efficacy of the surface modification of fly ash by quarternary ammonium cations in the removal of dyes from aqueous solution is demonstrated. A series of organo-fly ash materials were synthesized by treating fly ash with quarternary ammonium cations such as tetraethylammonium, hexadecyltrimethylammonium, and benzyldimethyltetradecylammonium (TEA, HDTMA, and BDTDA). Two types of dyes were used for the investigation, disperse and anionic dyes. The effects of initial dye concentration, contact time, temperature, and the mechanism of dye sorption were investigated. The sorption was found to be affected by the structure and size of the quaternary ammonium cations as well as that of the dyes. Sorption of dyes was considerably enhanced by the surface modification. Thermodynamic parameters such as free energy (DeltaG0), enthalpy (DeltaH0), and entropy (DeltaS0) for the sorption process were also calculated.     

Oxidation of alkyl aromatics to ketones by tert-butyl hydroperoxide on manganese dioxide catalyst

The catalytic activity of the manganese oxide was investigated for the oxidative functionalization of alkylaromatics to benzylic ketones using tert-butyl hydroperoxide (TBHP) as an oxidant. Manganese oxides of different types were tested for this reaction. Of all the oxides, the nano amorphous manganese dioxide exhibited significant catalytic activity and selectivity for the reaction. The nano amorphous MnO₂/TBHP catalytic system could also be reused for six consecutive cycles with no considerable loss in catalytic activity.     

Kinetics of cerium(IV) oxidation of macrocyclic complexes of chromium(III) and fate of chromium(IV) intermediates

Kinetics and mechanism of the cerium(IV) oxidation of Cr(III) complexes of a series of macrocyclic (or pseudomacrocyclic) ligands with [14]-membered intraligand ring-sizes have now been investigated at I = 1.0 M (LiClO₄) Temp. 30°C. The complexes of the formulation Cr(macrocycle)(X)(H₂O) where X = CHCl₂ and H₂O, n = 0 or 1 undergo oxidation to Cr(VI) with the formation of chromium(IV) intermediates. The observed kinetic parameters for the Ce(IV) oxidation of Cr(III) macrocyclic complexes have been discussed in terms of changes brought about by the macrocyclic ligands on the Cr(III)—Cr(IV) redox potentials and in specific rates for Cr(IV)—Cr(V) conversion. On the basis of this study, it has been suggested that the trapping of Cr(IV) is easier when a macrocyclic ligand having a symmetrical intra-ligand ring size and unsaturation in the cyclic structure is coordinated equatorially. Cyclic voltammetric studies indicate the formation of Cr(IV) transient in the case of electrochemical oxidation of trans-Cr(Me₄[14]tetraene)(H₂O).     

On identical nature of the superconductivity mechanisms in 30 K and 90 K superconductors

A systematic study of Zn substitution in both lanthanum and yttrium-based oxide superconductors withT _cof 30 K and 90 K has been carried out simultaneously under identical conditions. Contrary to the general belief, the results indicate that the mechanism responsible for superconductivity in 30 K compounds is unlikely to be radically different from that of the 90 K compounds.     

Singularities in Gaussian random fields

This paper studies a class of Gaussian random fields defined on lattices that arise in pattern analysis. Phase transitions are shown to exist at a critical temperature for these Gaussian random fields. These are established by showing discontinuous behavior for certain field random variables as the lattice size increases to infinity. The discontinuities in the statistical behavior of these random variables occur because the growth rates of the eigenvalues of the inverse of the variance-covariance matrix at the critical temperature are different from the growth rates at noncritical temperatures. It is also shown that the limiting specific heat has a phase transition with a power law behavior. The critical temperature occurs at the end point of the available values of temperature. Thus, although the critical behavior is not extreme, caution should be exercised when using such models near critical temperatures.Research supported by AFOSR Grant No. 91-0048 and by USARO Grant No. DAAL03-90-G-0103.     

Synthesis and reactions of 4-vinyl pyridine derivatives of ruthenium(II)

4-Vinyl pyridine (4-Vp) reacts with RuHClCO(PPh₃)₃ (I) in THF to give RuHClCO(PPh₃)₂(4-Vp) (II, which reacts with sodium derivatives of bidentate chelating ligands to afford substitution products, [RuH(CO)(PPh₃)₂(L)]. The bindentate ligands used are 2-hydroxybenzaldehyde, 2-hydroxy-3-methoxybenzaldehyde, trifluorothenoylacetone and 8-hydroxyquinoline. Insertion reactions of the Ru---H bond of II with activated olefins such as acrylonitrile [giving RuCl(CO)(CH₃CHCN)(PPh₃)₂(4-Vp)], 2-vinyl pyridine, dimethyl fumarate and monobromodiethyl fumarate have been carried out to obtain chelated Ru---C bonded complexes. RuCl₂(PPh₃)₃ reacts with an excess of 4-Vp to give an octahedral ruthenium addition complex containing two vinyl pyridine ligands. The dimer [RuClCO(CH₃CHCN)(PPh₃)(4-Vp)]₂ is obtained by the reaction of [RuClCO(CH₃CHCN)(PPh₃)₂]₂ with an excess of 4-Vp. Stereochemical assignments have been made for these new complexes on the basis of IR and ¹H NMR data.