CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone H-1(alpha) and C-13' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to alpha-helical/beta-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment.

Strategies for collecting screen-less oscillation data

Screen-less oscillation photography is the method of choice for recording three-dimensional X-ray diffraction data for crystals of biological macromolecules. The geometry of an oscillation camera is extremely simple. However, the manner in which the reciprocal lattice is recorded in any experiment is fairly complex. This depends on the Laue symmetry of the reciprocal lattice, the lattice type, the orientation of the crystal on the camera and to a lesser extent on the unit-cell dimensions. Exploring the relative efficiency of collecting X-ray diffraction data for different crystal orientations prior to data collection might reduce the number of films required to record most of the unique data and the consequent amount of time required for processing these films. Here algorithms are presented suitable for this purpose and results are reported for the 11 Laue groups, different lattice types and crystal orientations often employed in data collection.

On the functional ordering of biomembranes : Implications for drug binding

Cells are packed with membrane structures, defining the inside and outside, and the different subcellular compartments. These membranes consisting mainly of phospholipids have a variety of functions in addition to providing a permeability barrier for various compounds. These functions involve cellular signaling, where lipids can act as second messengers, or direct regulation of membrane associating proteins. The first part of this study focuses on relating some of the physicochemical properties of membrane lipids to the association of drug compounds to membranes. A fluorescence based method is described allowing for determination of the membrane association of drugs. This method was subsequently applied to a novel drug, siramesine, previously shown to have anti-cancer activity. Siramesine was found to associate with anionic lipids. Especially interesting is its strong affinity for a second messenger lipid phosphatidic acid. This is the first example of a small molecule drug compound specifically interacting with a cellular lipid. Phosphatidic acid in cells is required for the activation of many signaling pathways mediating growth and proliferation. This provides an intriguing possibility for a simple molecular mechanism of the observed anti-cancer activity of siramesine. In the second part the thermal behavior and self assembly of charged and uncharged membrane assemblies was studied. Strong inter-lamellar co-operativity was observed for multilamellar DPPC vesicles using fluorescence techniques together with calorimetry. The commonly used membrane models, large unilamellar vesicles (LUV) and multilamellar vesicles (MLV) were found to possess different biophysical properties as interlamellar interactions of MLVs drive segregation of a pyrene labeled lipid analogue into clusters. The effect of a counter-ion lattice on the self assembly of a cationic gemini surfactant was studied. The presence of NaCl strongly influenced the thermal phase behavior of M-1 vesicles, causing formation of giant vesicles upon exceeding a phase transition temperature, followed by a subsequent transition into a more homogenous dispersion. Understanding the underlying biophysical aspects of cellular membranes is of fundamental importance as the complex picture of the structure and function of cells is evolving. Many of the cellular reactions take place on membranes and membranes are known to regulate the activity of many peripheral and intergral membrane associating proteins. From the point of view of drug design and gene technology, membranes can provide an interesting target for future development of drugs, but also a vehicle sensitive for environmental changes allowing for encapsulating drugs and targeting them to the desired site of action.

Proton Spin-Lattice Relaxation in Sodium Ammonium Selenate Dihydrate:NaNHaSeOa.2He0

Proton spin-lattice relaxation studies in sodium ammonium selenate dihydrate carried out in the temperature range 130 to 300 K at 10 MHz show a continuous change in T, at T, indicating a second order phase transition. This compound is a typical case of a highly hindered solid wherein the thermally activated reorientations of ammonium ions freeze well above 77 K, as seen by NMR.Untersuchimgen der Protonen-Spin-Gitter-Relaxation in Natriuni-Ammoniumselenat-Dihydrat bei 10 MHz im Temperaturbereich 130 bis 300 K zeigen eine kontinuierliche Andernng in TI bei T, und ergeben einen Phasenubergang zweiter Art. Diese Verbindung ist ein typischer Fall eines stark ,,behinderten" Festkarpers, in dein die thermisch aktivierten Reorientierungen der Ammoniumionen weit oberhalb 77 H einfrieren, wie die NMR-Ergebnisse zeigen.

Aerodynamic characteristics of pretensioned elastic membrane rectangular sailwings

Presented in the paper are the details of a method for obtaining aerodynamic characteristics of pretensioned elastic membrane rectangular sailwings. This is a nonlinear problem governed by the membrane equation for the inflated sail and the lifting surface theory integral equation for aerodynamic loads on the sail. Assuming an admissible mode shape for the inflated elastic sail, an iterative procedure based on a doublet lattice method is employed to determine the inflated configuration as well as various aerodynamic characteristics. Application of the method is made to a typical nylon-cotton sailwing of AR = 6.0 and results are presented graphically to show the effect of various parameters. The results are found to tend to plane wing values when the pretensions are large in magnitude.

Non-Destructive Method to Estimate the Moisture Content in Bread using Multi-Channel Electrical Impedance Spectroscopy

Bread undergoes several physicochemical changes during storage that results in a rapid loss of freshness. These changes depend on moisture content present in bread product. An instrument based on electrical impedance spectroscopy technique is developed to estimate moisture content of bread at different zones using designed multi-channel ring electrodes. A dedicated AT89S52 microcontroller and associated peripherals are employed for hardware. A constant current is applied across bread loaf through central pair of electrodes and developed potential across different zones of bread loaf are measured using remaining four ring electrode pairs. These measured values of voltage and current are used to measure the impedance at each zone. Electrical impedance behavior of the bread loaf at crust and crumb is investigated during storage. A linear relationship is observed between the measured impedance and moisture content present in crust and crumb of bread loaf during storage of 120 hours.

Stability of Slopes by Method of Characteristics

The method of characteristics with some simplifying assumptions is made applicable for analyzing a given straight slope. By assuming that the mobilized shear strength varies with depth, and treating the whole soil mass as a series of layers, factors of safety of a given slope at different heights and a series of lines with different mobilized shear strength are obtained. The results show that the factors of safety obtained by the present method are lower than those obtained by friction circle method.

New method of calculating calorific values from elemental compositions of fossil fuels

A new method of calculating the calorific values of fossil fuels from their chemical composition has been developed, based on the concept that heats of reaction of stoichiometric fuel-oxidizer systems are rectilinearly related with the total oxidizing or reducing valancies of the mixture. The calorific value of fossil fuels has been shown to be directly related to the net reducing valencies of the fuel. The proposed method is simple and compares favourably with the other prominent methods reported in the literature.

An explicit finite element modelling method for masonry walls under out-of-plane loading

An explicit finite element modelling method is formulated using a layered shell element to examine the behaviour of masonry walls subject to out-of-plane loading. Masonry is modelled as a homogenised material with distinct directional properties that are calibrated from datasets of a “C” shaped wall tested under pressure loading applied to its web. The predictions of the layered shell model have been validated using several out-of-plane experimental datasets reported in the literature. Profound influence of support conditions, aspect ratio, pre-compression and opening to the strength and ductility of masonry walls is exhibited from the sensitivity analyses performed using the model.

Validation of a partial coherence interferometry method for estimating retinal shape

To validate a simple partial coherence interferometry (PCI) based retinal shape method, estimates of retinal shape were determined in 60 young adults using off-axis PCI, with three stages of modeling using variants of the Le Grand model eye, and magnetic resonance imaging (MRI). Stage 1 and 2 involved a basic model eye without and with surface ray deviation, respectively and Stage 3 used model with individual ocular biometry and ray deviation at surfaces. Considering the theoretical uncertainty of MRI (12-14%), the results of the study indicate good agreement between MRI and all three stages of PCI modeling with <4% and <7% differences in retinal shapes along horizontal and vertical meridians, respectively. Stage 2 and Stage 3 gave slightly different retinal co-ordinates than Stage 1 and we recommend the intermediate Stage 2 as providing a simple and valid method of determining retinal shape from PCI data.

On the Transform Method of Solution of an External Crack Problem

The breakdown of the usual method of Fourier transforms in the problem of an external line crack in a thin infinite elastic plate is discovered and the correct solution of this problem is derived using the concept of a generalised Fourier transform of a type discussed first by Golecki [1] in connection with Flamant's problem.