Luffa acutangula agglutinin: Primary structure determination and identification of a tryptophan residue involved in its carbohydrate-binding activity using mass spectrometry

A lectin from phloem exudates of Luffa acutangula (ridge gourd) was purified on chitin affinity chromatography and characterized for its amino acid sequence and to study the role of tryptophan in its activity. The purified lectin was subjected to various proteolytic digestions, and the resulting peptides were analyzed by liquid chromatography coupled electrospray ionization ion trap mass spectrometer. The peptide precursor ions were fragmented by collision-induced dissociation or electron transfer dissociation experiments, and a manual interpretation of MS/MS was performed to deduce amino acid sequence. This gave rise to almost complete sequence coverage of the lectin which showed high-sequence similarity with deduced sequences of phloem lectins present in the database. Chemical modification of lysine, tyrosine, histidine, arginine, aspartic acid, and glutamic acid residues did not inhibit the hemagglutinating activity. However, the modification of tryptophan residues using N-bromosuccinimide showed the loss of hemagglutinating activity. Additionally, the mapping of tryptophan residues was performed to determine the extent and number of residues modified, which revealed that six residues per molecule were oxidized suggesting their accessibility. The retention of the lectin activity was seen when the modifications were performed in the presence of chitooligosaccharides due to protection of a tryptophan residue (W-102) in the protein. These studies taken together have led to the identification of a particular tryptophan residue (W-102) in the activity of the lectin. (c) 2015 IUBMB Life, 67(12):943-953, 2015

Differential binding of ppGpp and pppGpp to E-coli RNA polymerase: photo-labeling and mass spectral studies

(p) ppGpp, a secondary messenger, is induced under stress and shows pleiotropic response. It binds to RNA polymerase and regulates transcription in Escherichia coli. More than 25 years have passed since the first discovery was made on the direct interaction of ppGpp with E. coli RNA polymerase. Several lines of evidence suggest different modes of ppGpp binding to the enzyme. Earlier cross-linking experiments suggested that the beta-subunit of RNA polymerase is the preferred site for ppGpp, whereas recent crystallographic studies pinpoint the interface of beta'/omega-subunits as the site of action. With an aim to validate the binding domain and to follow whether tetra-and pentaphosphate guanosines have different location on RNA polymerase, this work was initiated. RNA polymerase was photo-labeled with 8-azido-ppGpp/8-azido-pppGpp, and the product was digested with trypsin and subjected to mass spectrometry analysis. We observed three new peptides in the trypsin digest of the RNA polymerase labeled with 8-azido-ppGpp, of which two peptides correspond to the same pocket on beta'-subunit as predicted by X-ray structural analysis, whereas the third peptide was mapped on the beta-subunit. In the case of 8-azido-pppGpp-labeled RNA polymerase, we have found only one cross-linked peptide from the beta'-subunit. However, we were unable to identify any binding site of pppGpp on the beta-subunit. Interestingly, we observed that pppGpp at high concentration competes out ppGpp bound to RNA polymerase more efficiently, whereas ppGpp cannot titrate out pppGpp. The competition between tetraphosphate guanosine and pentaphosphate guanosine for E. coli RNA polymerase was followed by gel-based assay as well as by a new method known as DRaCALA assay.

Reply to Discussion on ``Bearing capacity of circular footings over rock mass by using axisymmetric quasi lower bound finite element limit analysis'' Comput. Geotech. 70 (2015) 138-149]

A discussion has been provided for the comments raised by the discusser (Clausen, 2015)1] on the article recently published by the authors (Chakraborty and Kumar, 2015). The effect of exponent alpha for values of GSI approximately smaller than 30 becomes more critical. On the other hand, for greater values of GSI, the results obtained by the authors earlier remain primarily independent of alpha and can be easily used. (C) 2015 Elsevier Ltd. All rights reserved.

Mass spectrometric analysis of dimer-disrupting mutations in Plasmodium triosephosphate isomerase

Electrospray ionization mass spectrometry (ESI MS) under nanospray conditions has been used to examine the effects of mutation at two key dimer interface residues, Gln (Q) 64 and Thr (T) 75, in Plasmodium falciparum triosephosphate isomerase. Both residues participate in an intricate network of intra- and intersubunit hydrogen bonds. The gas phase distributions of dimeric and monomeric protein species have been examined for the wild type enzyme (TWT) and three mutants, Q64N, Q64E, and 175S, under a wide range of collision energies (40-160 eV). The results established the order of dimer stability as TWT > T75S > Q64E similar to Q64N. The mutational effects on dimer stability are in good agreement with the previously reported estimates, based on the concentration dependence of enzyme activity. Additional experiments in solution, using inhibition of activity by a synthetic dimer interface peptide, further support the broad agreement between gas phase and solution studies. (C) 2016 Elsevier Inc. All rights reserved.

Effect of Rock Mass Structure and Block Size on the Slope Stability-Physical Modeling and Discrete Element Simulation

This paper studies the stability of jointed rock slopes by using our improved three-dimensional discrete element methods (DEM) and physical modeling. Results show that the DEM can simulate all failure modes of rock slopes with different joint configurations. The stress in each rock block is not homogeneous and blocks rotate in failure development. Failure modes depend on the configuration of joints. Toppling failure is observed for the slope with straight joints and sliding failure is observed for the slope with staged joints. The DEM results are also compared with those of limit equilibrium method (LEM). Without considering the joints in rock masses, the LEM predicts much higher factor of safety than physical modeling and DEM. The failure mode and factor of safety predicted by the DEM are in good agreement with laboratory tests for any jointed rock slope.

Experimental Studies of the Material Properties of the Forewing of Cicada (Homoptera, Cicadidae)

Detailed investigations on the structural and mechanical properties of the forewing of the cicada were carried out. Measurement of the structures of the wings showed that the thickness of the membrane of each cell and the diameter of each vein were non-uniform in both the longitudinal and transverse directions, and their means were approximately 12.2 and 133.3 mum, respectively. However, the aspect ratios of the wings and the bodies were quite uniform and were approximately equal to 2.98 and 2.13, respectively. Based on the measured thickness, mass and area of the membranes of the cells, the mean density and the mean area density of the wing were approximately 2.3 g cm(-3) and 2.8 x 10(-3) g cm(-2), respectively. In addition, the diameters of the veins of the wings, including the diameters of the holes in the vein of the leading edge, were examined. The mechanical properties of the wing were investigated separately by nanoindentation and tensile testing. The results indicated that the mean Young's modulus, hardness and yield stress of the membranes of the wings were approximately 3.7 Gpa, 0.2 Gpa and 29 Mpa, respectively, and the mean Young's modulus and strength of the veins along the direction of the venation of wings were approximately 1.9 Gpa and 52 Mpa, respectively. Finally, the relevant results were briefly analyzed and discussed, providing a guideline to the biomimetic design of the aerofoil materials of micro air vehicles.

Gal(1-x)Mn(1-x)Sb Grown on GaSb with Mass-Analyzed Low-Energy Dual Ion Beam Deposition

The Ga1-xMnxSb samples were fabricated by the implantation of Mn ions into GaSb (1 0 0) substrate with mass-analyzed low-energy dual ion beam deposition system, and post-annealing. Auger electron spectroscopy depth profile of the Ga1-xMnxSb samples showed

Conjugate Model for Heat and Mass Transfer of Porous Wall in the High Temperature Gas Flow

Heat and mass transfer of a porous permeable wall in a high temperature gas dynamical flow is considered. Numerical simulation is conducted on the ground of the conjugate mathematical model which includes filtration and heat transfer equations in a porous body and boundary layer equations on its surface. Such an approach enables one to take into account complex interaction between heat and mass transfer in the gasdynamical flow and in the structure subjected to this flow. The main attention is given to the impact of the intraporous heat transfer intensity on the transpiration cooling efficiency.

Iterative method using consistent mass matrix in axisymmetrical finite element analysis of hypervelocity impact

We present in this paper an iterative method using consistent mass matrix in axisymmetrical finite element analysis of hypervelocity impact. To retain the advantage of integration on an element-by-element basis which is at the heart of modern hydrocodes, we suggest that the first step should be to solve for accelerations at an advanced time step by using the lumped mass approach, then iterate using a consistent mass matrix to improve the estimate. Examples are given to show the improved resolution with the new method.

Kinetic Assessment of Measured Mass Flow Rates and Streamwise Pressure Distributions in Microchannel Gas Flows

Measured mass flow rates and streamwise pressure distributions of gas flowing through microchannels were reported by many researchers. Assessment of these data is crucial before they are used in the examination of slip models and numerical schemes, and in the design of microchannel elements in various MEMS devices. On the basis of kinetic solutions of the mass flow rates and pressure distributions in microchannel gas flows, the measured data available are properly normalized and then are compared with each other. The 69 normalized data of measured pressure distributions are in excellent agreement, and 67 of them are within 1 +/- 0.05. The normalized data of mass flow-rates ranging between 0.95 and 1 agree well with each other as the inlet Knudsen number Kn (i) < 0.02, but they scatter between 0.85 and 1.15 as Kn (i) > 0.02 with, to some extent, a very interesting bifurcation trend.

Thin film monitoring with silicon bulk acoustic resonators

Abstract-This paper reports a single-crystal silicon mass sensor based on a square-plate resonant structure excited in the wine glass bulk acoustic mode at a resonant frequency of 2.065 MHz and an impressive quality factor of 4 million at 12 mtorr pressure. Mass loading on the resonator results in a linear downshift in the resonant frequency of this device, wherein the measured sensitivity is found to be 175 Hz cm2/μg. The silicon resonator is embedded in an oscillator feedback loop, which has a short-term frequency stability of 3 mHz (approximately 1.5 ppb) at an operating pressure of 3.2 mtorr, corresponding to an equivalent mass noise floor of 17 pg/cm2. Possible applications of this device include thin film monitoring and gas sensing, with the potential added benefits of scalability and integration with CMOS technology. © 2008 IEEE.