NMRof peptides

Developments and applications of NMR spectroscopy especially with biomolecules has taken big strides over the decades. This review gives a brief overview of peptide analysis by NMR as carried out in the author’s laboratory. A brief introduction to peptide biomolecules and NMR useful parameters are discussed in the beginning. This is followed by diagnostics features observed in NMR for identification of secondary structures. It further goes on to show how a three dimensional structure could be obtained by all-important NOE and hydrogen bond information. Use of heteronuclear experiments, which could be done at natural abundance is also highlighted in getting more details of peptide structures.Applications using Solid state NMR at natural abundance in connecting peptide solution and x-ray structures is demonstrated with couple of examples.

Two-dimensional approximations of 3-dimensional eigenvalue problems in plate-theory

The eigenvalues and eigenfunctions corresponding to the three-dimensional equations for the linear elastic equilibrium of a clamped plate of thickness 2ϵ, are shown to converge (in a specific sense) to the eigenvalues and eigenfunctions of the well-known two-dimensional biharmonic operator of plate theory, as ϵ approaches zero. In the process, it is found in particular that the displacements and stresses are indeed of the specific forms usually assumed a priori in the literature. It is also shown that the limit eigenvalues and eigenfunctions can be equivalently characterized as the leading terms in an asymptotic expansion of the three-dimensional solutions, in terms of powers of ϵ. The method presented here applies equally well to the stationary problem of linear plate theory, as shown elsewhere by P. Destuynder.

On the solution of bivariate population balance equations for aggregation: X-discretization of space for expansion and contraction of computational domain

A new structured discretization of 2D space, named X-discretization, is proposed to solve bivariate population balance equations using the framework of minimal internal consistency of discretization of Chakraborty and Kumar [2007, A new framework for solution of multidimensional population balance equations. Chem. Eng. Sci. 62, 4112-4125] for breakup and aggregation of particles. The 2D space of particle constituents (internal attributes) is discretized into bins by using arbitrarily spaced constant composition radial lines and constant mass lines of slope -1. The quadrilaterals are triangulated by using straight lines pointing towards the mean composition line. The monotonicity of the new discretization makes is quite easy to implement, like a rectangular grid but with significantly reduced numerical dispersion. We use the new discretization of space to automate the expansion and contraction of the computational domain for the aggregation process, corresponding to the formation of larger particles and the disappearance of smaller particles by adding and removing the constant mass lines at the boundaries. The results show that the predictions of particle size distribution on fixed X-grid are in better agreement with the analytical solution than those obtained with the earlier techniques. The simulations carried out with expansion and/or contraction of the computational domain as population evolves show that the proposed strategy of evolving the computational domain with the aggregation process brings down the computational effort quite substantially; larger the extent of evolution, greater is the reduction in computational effort. (C) 2011 Elsevier Ltd. All rights reserved.

Hydrolysis of Ammonia Borane as a Hydrogen Source: Fundamental Issues and Potential Solutions Towards Implementation

In todays era of energy crisis and global warming, hydrogen has been projected as a sustainable alternative to depleting CO2-emitting fossil fuels. However, its deployment as an energy source is impeded by many issues, one of the most important being storage. Chemical hydrogen storage materials, in particular B?N compounds such as ammonia borane, with a potential storage capacity of 19.6 wt?% H2 and 0.145 kg?H?2?L-1, have been intensively studied from the standpoint of addressing the storage issues. Ammonia borane undergoes dehydrogenation through hydrolysis at room temperature in the presence of a catalyst, but its practical implementation is hindered by several problems affecting all of the chemical compounds in the reaction scheme, including ammonia borane, water, borate byproducts, and hydrogen. In this Minireview, we exhaustively survey the state of the art, discuss the fundamental problems, and, where applicable, propose solutions with the prospect of technological applications.

Site-specific N-Linked Glycosylation of Receptor Guanylyl Cyclase C Regulates Ligand Binding, Ligand-mediated Activation and Interaction with Vesicular Integral Membrane Protein 36, VIP36

Guanylyl cyclase C (GC-C) is a multidomain, membrane-associated receptor guanylyl cyclase. GC-C is primarily expressed in the gastrointestinal tract, where it mediates fluid-ion homeostasis, intestinal inflammation, and cell proliferation in a cGMP-dependent manner, following activation by its ligands guanylin, uroguanylin, or the heat-stable enterotoxin peptide (ST). GC-C is also expressed in neurons, where it plays a role in satiation and attention deficiency/hyperactive behavior. GC-C is glycosylated in the extracellular domain, and differentially glycosylated forms that are resident in the endoplasmic reticulum (130 kDa) and the plasma membrane (145 kDa) bind the ST peptide with equal affinity. When glycosylation of human GC-C was prevented, either by pharmacological intervention or by mutation of all of the 10 predicted glycosylation sites, ST binding and surface localization was abolished. Systematic mutagenesis of each of the 10 sites of glycosylation in GC-C, either singly or in combination, identified two sites that were critical for ligand binding and two that regulated ST-mediated activation. We also show that GC-C is the first identified receptor client of the lectin chaperone vesicular integral membrane protein, VIP36. Interaction with VIP36 is dependent on glycosylation at the same sites that allow GC-C to fold and bind ligand. Because glycosylation of proteins is altered in many diseases and in a tissue-dependent manner, the activity and/or glycan-mediated interactions of GC-C may have a crucial role to play in its functions in different cell types.

Ductile fracture by multiple void growth and interaction ahead of a notch tip in polycrystalline plastic solids

The objectives of this paper are to study the effects of plastic anisotropy and evolution in crystallographic texture with deformation on the ductile fracture behaviour of polycrystalline solids. To this end, numerical simulations of multiple void growth and interaction ahead of a notch tip are performed under mode I, plane strain, small scale yielding conditions using two approaches. The first approach is based on the Hill yield theory, while the second employs crystal plasticity constitutive equations and a Taylor-type homogenization in order to represent the ductile polycrystalline solid. The initial textures pertaining to continuous cast Al-Mg AA5754 sheets in recrystallized and cold rolled conditions are considered. The former is nearly-isotropic, while the latter displays pronounced anisotropy. The results indicate distinct changes in texture in the ligaments bridging the voids ahead of the notch tip with increase in load level which gives rise to retardation in porosity evolution and increase in tearing resistance for both materials.

Revision of the scolopendrid centipede digitipes Attems, 1930, from India (Chilopoda: Scolopendromorpha): reconciling molecular and morphological estimates of species diversity

Recent work on molecular phylogenetics of Scolopendridae from the Western Ghats, Peninsular India, has suggested the presence of six cryptic species of the otostigmine Digitipes Attems, 1930, together with three species described in previous taxonomic work by Jangi and Dass (1984). Digitipes is the correct generic attribution for a monophyletic group of Indian species, these being united with three species from tropical Africa (including the type) that share a distomedial process on the ultimate leg femur of males that is otherwise unknown in Otostigminae. Second maxillary characters previously used in the diagnosis of Digitipes are dismissed because Indian species do not possess the putatively diagnostic character states. Two new species from the Western Ghats that correspond to groupings identified based on monophyly, sequence divergence and coalescent analysis using molecular data are diagnosed based on distinct morphological characters. They are D. jangii and D. periyarensis n. spp. Three species named by Jangi and Dass (Digitipes barnabasi, D. coonoorensis and D. indicus) are revised based on new collections; D. indicus is a junior subjective synonym of Arthrorhabdus jonesii Verhoeff, 1938, the combination becoming Digitipes jonesii (Verhoeff, 1938) n. comb. The presence of Arthrorhabdus in India is accordingly refuted. Three putative species delimited by molecular and ecological data remain cryptic from the perspective of diagnostic morphological characters and are presently retained in D. barnabasi, D. jangii and D. jonesii. A molecularly-delimited species that resolved as sister group to a well-supported clade of Indian Digitipes is identified as Otostigmus ruficeps Pocock, 1890, originally described from a single specimen and revised herein. One Indian species originally assigned to Digitipes, D. gravelyi, deviates from confidently-assigned Digitipes with respect to several characters and is reassigned to Otostigmus, as O. gravelyi (Jangi and Dass, 1984) n. comb.

Ferromagnetic Resonance Study on a Grid of Permalloy Nanowires

We report ferromagnetic resonance (FMR) study on a grid formed with permalloy nanowires to understand the spin wave dynamics. The presence of two sets of magnetic nanowires perpendicular to each other in the same device enables better control over spin waves. The grid was fabricated using e-beam lithography followed by DC-Magnetron sputtering and liftoff technique. It has dimensions of 800 +/- 10 and 400 +/- 10 nm as periods along X and Y directions with permalloy wires of width 145 +/- 10 nm. FMR studies were done at X-band (9.4 GHz) with the field sweep up to 1 Tesla. The in-plane angular variation of resonant fields shows that there are two well separated modes present, indicating two uniaxial anisotropy axes which are perpendicular to each other. The variation in the intensities in the FMR signal w.r.t. the grid angle is used to describe the spin wave confinement in different regions of the grid. We also explained the asymmetry in the magnetic properties caused by the geometrical property of the rectangular grid and the origin for the peak splitting for the modes occurring at higher resonant fields. Micromagnetic simulations based on OOMMF with two dimensional periodic boundary conditions (2D-PBC) are used to support our experimental findings.

DEPRESSION OF MAGNETlCALLY FIXED EMISSION ZONE IN LOW PRESSURE MERCURY ARCS

A transverse magnetic field was used to fix the cathode spot of a low pressure mercury arc with liquid cathode It was noticed that such fixation causes consider-abledepression of the emission zone below the mercury level.This depression varies with the arc current and the magnetic field and is associated with an increase in the arc voltage drop. It indicates appreciable pressure in the emission zone.

Nonlinear gravity-wave interactions in stratified turbulence

To investigate the dynamics of gravity waves in stratified Boussinesq flows, a model is derived that consists of all three-gravity-wave-mode interactions (the GGG model), excluding interactions involving the vortical mode. The GGG model is a natural extension of weak turbulence theory that accounts for exact three-gravity-wave resonances. The model is examined numerically by means of random, large-scale, high-frequency forcing. An immediate observation is a robust growth of the so-called vertically sheared horizontal flow (VSHF). In addition, there is a forward transfer of energy and equilibration of the nonzero-frequency (sometimes called ``fast'') gravity-wave modes. These results show that gravity-wave-mode interactions by themselves are capable of systematic interscale energy transfer in a stratified fluid. Comparing numerical simulations of the GGG model and the full Boussinesq system, for the range of Froude numbers (Fr) considered (0.05 a parts per thousand currency sign Fr a parts per thousand currency sign 1), in both systems the VSHF is hardest to resolve. When adequately resolved, VSHF growth is more vigorous in the GGG model. Furthermore, a VSHF is observed to form in milder stratification scenarios in the GGG model than the full Boussinesq system. Finally, fully three-dimensional nonzero-frequency gravity-wave modes equilibrate in both systems and their scaling with vertical wavenumber follows similar power-laws. The slopes of the power-laws obtained depend on Fr and approach -2 (from above) at Fr = 0.05, which is the strongest stratification that can be properly resolved with our computational resources.

High-Resolution Solid State C-13 NMR Studies of Bent-Core Mesogens of Benzene and Thiophene

Bent-core mesogens are an important class of thermotropic liquid crystals as they exhibit unusual properties as well as morphologies distinctly different from rodlike mesogens. Two bent-core mesogens with differing center rings namely benzene and thiophene are considered and investigated using high-resolution oriented solid state C-13 NMR method in their liquid crystalline phases. The mesogens exhibit different phase sequences with the benzene-based mesogen showing a B-1 phase, while the one based on thiophene showing nematic and smectic C phases. The 2-dimensional separated local field (2D-SLF) NMR method was used to obtain the C-13-H-1 dipolar couplings of carbons in the center ring as well as in the side-wing phenyl rings. Couplings, characteristic of the type of the center ring, that also provide orientational information on the molecule in the magnetic field were observed. Together with the dipolar couplings of the side-wing phenyl ring carbons from which the local order parameters of the different subunits of the core could be extracted, the bent angle of the mesogenic molecule could be obtained. Accordingly, for the benzene mesogen in its B-1 phase at 145 degrees C, the center ring methine C-13-H-1 dipolar couplings were found to be significantly larger (9.5-10.2 kHz) compared to those of the side-wing rings (1.6-2.1 kHz). From the local order parameter values of the center (0.68) as well as the side-wing rings (0.50), a bent-angle of 130.3 degrees for this mesogen was obtained. Interestingly, for the thiophene mesogen in its smectic C phase at 210 degrees C, the C-13-H-1 dipolar coupling of the center ring methine carbon (2.11 kHz) is smaller than those of the side-wing phenyl ring carbons (2.75-3.00 kHz) which is a consequence of the different structures of the thiophene and the benzene rings. These values correspond to local order parameters of 0.85 for the center thiophene ring and 0.76 for the first side-wing phenyl ring and a bent-angle of 149.2 degrees. Thus, the significant differences in the dipolar couplings and the order parameter values between different parts in the rigid core of the mesogens are a direct consequence of the nature of the center ring and the bent structure of the molecule. The present investigation thus highlights the ability of the C-13 2D-SLF technique to provide the geometry of the bent-core mesogens in a straightforward manner through the measurement of the C-13-H-1 dipolar couplings.