Ricin-membrane interaction: membrane penetration depth by fluorescence quenching and resonance energy transfer

The entry of the plant toxin ricin and its A- and B-subunits in model membranes in the presence as well as absence of monosialoganglioside (GM(1)) has been studied. Dioleoylphosphatidylcholine and 5-, 10-, and 12-doxyl- or 9,10-dibromophosphatidylcholines serve as quenchers of intrinsic tryptophan fluorescence of the proteins. The parallax method of Chattopadhyay and London [(1987) Biochemistry 26, 39-45] has been employed to measure the average membrane penetration depth of tryptophans of ricin and its B-chain and the actual depth of the sole Trp 211 in the A-chain. The results indicate that both of the chains as well as intact ricin penetrate the membrane deeply and the C-terminal end of the A-chain is well inside the bilayer, especially at pH 4.5. An extrinsic probe N-(iodoacetyl)-N'-(5-sulfo-1-naphthyl) ethylenediamine (I-AEDANS) has been attached to Cys 259 of the A-chain, and the kinetics of penetration has been followed by monitoring the increase in AEDANS fluorescence at 480 nm. The insertion follows first-order kinetics, and the rate constant is higher at a lower pH. The energy transfer distance analysis between Trp 211 and AEDANS points out that the conformation of the A-chain changes as it inserts into the membrane. CD studies indicate that the helicity of the proteins increases after penetration, which implies that some of the unordered structure in the native protein is converted to the ordered form during this process. Hydrophobic forces seem to be responsible for stabilizing a particular protein conformation inside the membrane.

Parallel computing concepts and methods for floquet analysis of helicopter trim and stability

Floquet analysis is widely used for small-order systems (say, order M < 100) to find trim results of control inputs and periodic responses, and stability results of damping levels and frequencies, Presently, however, it is practical neither for design applications nor for comprehensive analysis models that lead to large systems (M > 100); the run time on a sequential computer is simply prohibitive, Accordingly, a massively parallel Floquet analysis is developed with emphasis on large systems, and it is implemented on two SIMD or single-instruction, multiple-data computers with 4096 and 8192 processors, The focus of this development is a parallel shooting method with damped Newton iteration to generate trim results; the Floquet transition matrix (FTM) comes out as a byproduct, The eigenvalues and eigenvectors of the FTM are computed by a parallel QR method, and thereby stability results are generated, For illustration, flap and flap-lag stability of isolated rotors are treated by the parallel analysis and by a corresponding sequential analysis with the conventional shooting and QR methods; linear quasisteady airfoil aerodynamics and a finite-state three-dimensional wake model are used, Computational reliability is quantified by the condition numbers of the Jacobian matrices in Newton iteration, the condition numbers of the eigenvalues and the residual errors of the eigenpairs, and reliability figures are comparable in both the parallel and sequential analyses, Compared to the sequential analysis, the parallel analysis reduces the run time of large systems dramatically, and the reduction increases with increasing system order; this finding offers considerable promise for design and comprehensive-analysis applications.

Computing Fractal Dimension of Signals using Multiresolution Box-counting Method

In this paper, we have developed a method to compute fractal dimension (FD) of discrete time signals, in the time domain, by modifying the box-counting method. The size of the box is dependent on the sampling frequency of the signal. The number of boxes required to completely cover the signal are obtained at multiple time resolutions. The time resolutions are made coarse by decimating the signal. The loglog plot of total number of boxes required to cover the curve versus size of the box used appears to be a straight line, whose slope is taken as an estimate of FD of the signal. The results are provided to demonstrate the performance of the proposed method using parametric fractal signals. The estimation accuracy of the method is compared with that of Katz, Sevcik, and Higuchi methods. In ddition, some properties of the FD are discussed.

Transmembrane domains participate in functions of integral membrane proteins

Integral membrane proteins have one or more transmembrane a-helical domains and carry out a variety of functions such as enzyme catalysis, transport across membranes, transducing signals as receptors of hormones and growth factors, and energy transfer in ATP synthesis. These transmembrane domains are not mere structural units anchoring the protein to the lipid bilayer but seem to-contribute in the overall activity. Recent findings in support of this are described using some typical examples-LDL receptor, growth factor receptor tyrosine kinase, HMG-CoA reductase, F-0-ATPase and adrenergic receptors. The trends in research indicate that these transmembrane domains participate in a variety of ways such as a linker, a transducer or an exchanger in the overall functions of these proteins in transfer of materials, energy and signals.

Synthesis and vesicle formation from novel pseudoglyceryl dimeric lipids. Evidence of formation of widely different membrane organizations with exceptional thermotropic properties

Eight new bis-cationic dimeric lipids 2a-h have been synthesized; TEM of their aqueous dispersions confirmed the vesicle formation and from the thermal, spectroscopic, DLS and XRD studies it has been revealed that they form three different kinds of membranous aggregate depending on the m-value.

Stability of fluid flow past a membrane

The stability of fluid flow past a membrane of infinitesimal thickness is analysed in the limit of zero Reynolds number using linear and weakly nonlinear analyses. The system consists of two Newtonian fluids of thickness R* and H R*, separated by an infinitesimally thick membrane, which is flat in the unperturbed state. The dynamics of the membrane is described by its normal displacement from the flat state, as well as a surface displacement field which provides the displacement of material points from their steady-state positions due to the tangential stress exerted by the fluid flow. The surface stress in the membrane (force per unit length) contains an elastic component proportional to the strain along the surface of the membrane, and a viscous component proportional to the strain rate. The linear analysis reveals that the fluctuations become unstable in the long-wave (alpha --> 0) limit when the non-dimensional strain rate in the fluid exceeds a critical value Lambda(t), and this critical value increases proportional to alpha(2) in this limit. Here, alpha is the dimensionless wavenumber of the perturbations scaled by the inverse of the fluid thickness R*(-1), and the dimensionless strain rate is given by Lambda(t) = ((gamma) over dot* R*eta*/Gamma*), where eta* is the fluid viscosity, Gamma* is the tension of the membrane and (gamma) over dot* is the strain rate in the fluid. The weakly nonlinear stability analysis shows that perturbations are supercritically stable in the alpha --> 0 limit.

Amino acid interaction preferences in helical membrane proteins

Membrane proteins are involved in a number of important biological functions. Yet, they are poorly understood from the structure and folding point of view. The external environment being drastically different from that of globular proteins, the intra-protein interactions in membrane proteins are also expected to be different. Hence, statistical potentials representing the features of inter-residue interactions based exclusively on the structures of membrane proteins are much needed. Currently, a reasonable number of structures are available, making it possible to undertake such an analysis on membrane proteins. In this study we have examined the inter-residue interaction propensities of amino acids in the membrane spanning regions of the alpha-helical membrane (HM) proteins. Recently we have shown that valuable information can be obtained on globular proteins by the evaluation of the pair-wise interactions of amino acids by classifying them into different structural environments, based on factors such as the secondary structure or the number of contacts that a residue can make. Here we have explored the possible ways of classifying the intra-protein environment of HM proteins and have developed scoring functions based on different classification schemes. On evaluation of different schemes, we find that the scheme which classifies amino acids to different intra-contact environment is the most promising one. Based on this classification scheme, we also redefine the hydrophobicity scale of amino acids in HM proteins.

Efficient Algorithms for Computing All Low s-t Edge Connectivities and Related Problems

Given an undirected unweighted graph G = (V, E) and an integer k ≥ 1, we consider the problem of computing the edge connectivities of all those (s, t) vertex pairs, whose edge connectivity is at most k. We present an algorithm with expected running time Õ(m + nk3) for this problem, where |V| = n and |E| = m. Our output is a weighted tree T whose nodes are the sets V1, V2,..., V l of a partition of V, with the property that the edge connectivity in G between any two vertices s ε Vi and t ε Vj, for i ≠ j, is equal to the weight of the lightest edge on the path between Vi and Vj in T. Also, two vertices s and t belong to the same Vi for any i if and only if they have an edge connectivity greater than k. Currently, the best algorithm for this problem needs to compute all-pairs min-cuts in an O(nk) edge graph; this takes Õ(m + n5/2kmin{k1/2, n1/6}) time. Our algorithm is much faster for small values of k; in fact, it is faster whenever k is o(n5/6). Our algorithm yields the useful corollary that in Õ(m + nc3) time, where c is the size of the global min-cut, we can compute the edge connectivities of all those pairs of vertices whose edge connectivity is at most αc for some constant α. We also present an Õ(m + n) Monte Carlo algorithm for the approximate version of this problem. This algorithm is applicable to weighted graphs as well. Our algorithm, with some modifications, also solves another problem called the minimum T-cut problem. Given T ⊆ V of even cardinality, we present an Õ(m + nk3) algorithm to compute a minimum cut that splits T into two odd cardinality components, where k is the size of this cut.

Bio-Composite Membrane Electrolytes for Direct Methanol Fuel Cells

A new class of bio-composite polymer electrolyte membranes comprising chitosan (CS) and certain biomolecules in particular, plant hormones such as 3-indole acetic acid (IAA), 4-chlorophenoxy acetic acid (CAA) and 1-naphthalene acetic acid (NAA) are explored to realize proton-conducting bio-composite membranes for application in direct methanol fuel cells (DMFCs). The sorption capability, proton conductivity and ion-exchange capacity of the membranes are characterized in conjunction with their thermal and mechanical behaviour. A novel approach to measure the permeability of the membranes to both water and methanol is also reported, employing NMR imaging and volume localized NMR spectroscopy, using a two compartment permeability cell. A DMFC using CS-IAA composite membrane, operating with 2M aqueous methanol and air at 70 degrees C delivers a peak power density of 25 mW/cm(2) at a load current density of 150 mA/cm(2). The study opens up the use of bio-compatible membranes in polymer-electrolyte-membrane fuel cells. (C) 2011 The Electrochemical Society. [DOI: 10.1149/2.030111jes] All rights reserved.

Editorial optical computing circuits, devices and systems

Information forms the basis of modern technology. To meet the ever-increasing demand for information, means have to be devised for a more efficient and better-equipped technology to intelligibly process data. Advances in photonics have made their impact on each of the four key applications in information processing, i.e., acquisition, transmission, storage and processing of information. The inherent advantages of ultrahigh bandwidth, high speed and low-loss transmission has already established fiber-optics as the backbone of communication technology. However, the optics to electronics inter-conversion at the transmitter and receiver ends severely limits both the speed and bit rate of lightwave communication systems. As the trend towards still faster and higher capacity systems continues, it has become increasingly necessary to perform more and more signal-processing operations in the optical domain itself, i.e., with all-optical components and devices that possess a high bandwidth and can perform parallel processing functions to eliminate the electronic bottleneck.