Analysis of proteins with the `hot dog' fold: Prediction of function and identification of catalytic residues of hypothetical proteins

Background: The hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. The fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme A-binding enzymes with a variety of substrates located at their active sites. Results: We have analyzed the structural features and sequences of proteins having the hot dog fold. This study reveals that though the basic architecture of the fold is well conserved in these proteins, significant differences exist in their sequence, nature of substrate and oligomerization. Segments with certain conserved sequence motifs seem to play crucial structural and functional roles in various classes of these proteins. Conclusion: The analysis led to predictions regarding the functional classification and identification of possible catalytic residues of a number of hot dog fold-containing hypothetical proteins whose structures were determined in high throughput structural genomics projects.

Reaction of Hexachlorocyclotriphosphazene with Sodium p-Cresoxide

The reaction of hexachlorocyclotriphosphazene (N3P3Cl6) with sodium p-cresoxide proceeds by a predominantly nongeminal pathway. The presence of geminal isomers at the bis- and tris-stages of substitution in tiny quantities (< 5%) has also been observed. All the chloro(p-cresoxy)cyclotriphosphazenes and their dimethylamino derivatives have been characterized by 1H-, 13C{1H}-, and 31P{1H}-NMR spectroscopy. The reaction of N3P3Cl6 with sodium phenoxide has been reinvestigated. The relative yields of the products at various stages of substitution and their isomeric compositions are almost the same for both phenoxy and p-cresoxy systems. Possible mechanisms to explain the observed isomeric compositions are discussed. A through-space interaction involving oxygen-2p and phosphorus-3d orbitals is invoked to explain the greater yield of the cis isomer of N3P3Cl4(OAr)2 than that of its trans isomer.

Dynamic structure factor across the liquid-solid interface: appearance of a delta-function elastic peak

We present a theoretical calculation of the dynamic structure factor, S(k, ω), at the liquid-solid interface for large values of the wavevector k. An analytic expression is derived which shows the evolution of the elastic peak as the solid surface is approached from the liquid side.

Reaction of thiophosphoryl fluoride with sulphur trioxide

Thiophosphoryl fluoride is observed to undergo a facile reaction with sulphur trioxide forming phosphoryl fluoride, sulphur dioxide and elemental sulphur in quantitative yields. In the presence of excess of sulphur trioxide, however, the elemental sulphur released combines with it to form sulphur sesquioxide which subsequently decomposes and gives off sulphur dioxide. Similar observations are made with oleum.

Brownian particles in stationary and moving traps: The mean and variance of the heat distribution function

A recent theoretical model developed by Imparato et al. Phys of the experimentally measured heat and work effects produced by the thermal fluctuations of single micron-sized polystyrene beads in stationary and moving optical traps has proved to be quite successful in rationalizing the observed experimental data. The model, based on the overdamped Brownian dynamics of a particle in a harmonic potential that moves at a constant speed under a time-dependent force, is used to obtain an approximate expression for the distribution of the heat dissipated by the particle at long times. In this paper, we generalize the above model to consider particle dynamics in the presence of colored noise, without passing to the overdamped limit, as a way of modeling experimental situations in which the fluctuations of the medium exhibit long-lived temporal correlations, of the kind characteristic of polymeric solutions, for instance, or of similar viscoelastic fluids. Although we have not been able to find an expression for the heat distribution itself, we do obtain exact expressions for its mean and variance, both for the static and for the moving trap cases. These moments are valid for arbitrary times and they also hold in the inertial regime, but they reduce exactly to the results of Imparato et al. in appropriate limits. DOI: 10.1103/PhysRevE.80.011118 PACS.

Heats of reaction between aniline and formaldehyde by solution calorimetry: Reaction in neutral medium

The enthalpies of reaction between aniline and HCHO at various molar proportions under neutral conditions were determined by solution calorimetry. These measurements are new in the field of aniline and HCHO condensation polymers. The specific heats of the products formed were determined by differential scanning calorimetry and were used in the enthalpy calculations. Plots of enthalpy of reaction calculated with respect to aniline and HCHO vs. different A/F molar ratios were made. From the enthalpy data it appears that the reactions between different A/F molar ratios yield different products.

Metallo crown porphyrins as ionophores-metal dependent uncoupling of mitochondrial energy potential

Porphyrins appended with crown ether moieties function as efficient uncouplesrs of oxidative phorphorylation in rat liver mitochondria. Permeation of these highly organized porphyrins decrease the respiratory coefficient index (RCI) values. Lowering of the RCI values parallels the number of K+ chelating crown ether groups attached to the porphyrins. The inhibitory effect upon the oxidative phorphorylation reaction depends on the nature of divalent metal ions, VO, Co, Cu and Zn in the porphyrin cavity and related to their relative tendency to complex intracellular K+ ions.

A Branch and Bound Algorithm for a Transportation Type Problem with Piecewise Linear Convex Objective Function

A branch and bound type algorithm is presented in this paper to the problem of finding a transportation schedule which minimises the total transportation cost, where the transportation cost over each route is assumed to be a piecewice linear continuous convex function with increasing slopes. The algorithm is an extension of the work done by Balachandran and Perry, in which the transportation cost over each route is assumed to beapiecewise linear discontinuous function with decreasing slopes. A numerical example is solved illustrating the algorithm.

Reaction product of lime and silica from rice husk ash

Rice husk ash (about 95% silica) with known physical and chemical characteristics has been reacted with lime and water. The setting process for a lime-excess and a lime-deficient mixture has been investigated. The product of the reaction has been shown to be a calcium silicate hydrate, C-S-H(I)+ by a combination of thermal analysis, XRD and electron microscopy. Formation of C-S-H(I) accounts for the strength of lime-rice husk ash cement.

Applications of the Vilsmeier reaction. 13. Vilsmeier approach to polycyclic aromatic hydrocarbons

The Synthesis of three typical polycyclic hydrocarbons (PAH) has been described, wherein the Vilsmeier reaction plays a major role. Vilsmeier reaction of the tetraloll gives the dihydronaphthaldehyde 2 which on cyclodehydration gives the dihydroarene 3. Ita dehydrogenation affords 3-methoxybenz[a]anthracene (4). Vilsmeier reaction on the dimethoxydihydronaphthalene 5 gives the versatile dimethoxydihydronaphthaldehyde 6 which has been converted to the dimethoxybenzo[c]fluorene 7 by direct cyclodehydration and the fulvene 10 by cyclodehydration of allylic alcohol 8 derived from 6 followed by dehydrogenation. The saturated alcohol 12 corresponding to 8 undergoes cyclodehydration to give the dimethoxyhexahydrobenzo[c]phenanthrene (13). Some of the advantages of the Vilsmeier approach to PAH have been pointed out.

Photolysis of the dithiolactone 4-isopropylidene-3,3-dimethyl-1-thietan-2-thione; a Norrish type I reaction

The dithiolactone (1) upon excitation gives the dithione (2) in cyclohexane and other aprotic solvents and a 1 : 1 adduct in hydroxylic solvents from an n* excited singlet state via an -cleavage process.

Contributions to organic synthesis and reaction mechanisms

Development of new methods, leading to the first stereo-specific total synthesis of a steroid,viz equilenin, and of estrone and their derivatives and of several important synthones, useful for the preparation of physiologically active steroids, and the first conversion of an equilenane to estrane have been described. An account of the achievement of original syntheses of testosterone and its isomers and derivatives and degradation products, urinary steroids, terpenes and their important degradation products has been given. Mechanisms of Dieckmann cyclization, a novel dehydrogenation-addition reaction involving abietic acid and tetrachloro-o-benzoquinone, a rearrangement involving a substitution of cyclopentanone-2-carboxylic ester have been elucidated. An abnormaluv absorption exhibited by saturated 1,2-dicyano esters has been rationalized. Divergences in theord data of testosterone and 19-nortesto-sterone from their isomers have been explained by x-ray crystallographic studies of 8-isotestosterone, 8-iso-10-isotestosterone and 8-iso-10-iso-19-nortestosterone. A tentative explanation for the difference in their physiological activities has been suggested.

Approximate analysis of coupled non-linear non-conservative systems subjected to step-function excitation

The paper deals with the approximate analysis of non-linear non-conservative systems oftwo degrees of freedom subjected to step-function excitation. The method of averaging of Krylov and Bogoliubov is used to arrive at the approximate equations for amplitude and phase. An example of a spring-mass-damper system is presented to illustrate the method and a comparison with numerical results brings out the validity of the approach.