Multivalent ligand presentation as a central concept to study intricate carbohydrate-protein interactions

Studying the weak binding affinities between carbohydrates and proteins has been a central theme in sustained efforts to uncover intricate details of this class of biomolecular interaction. The amphiphilic nature of most carbohydrates, the competing nature of the surrounding water molecules to a given protein receptor site and the receptor binding site characteristics led to the realization that carbohydrates are required to exert favorable interactions, primarily through clustering of the ligands. The clustering of sugar ligands has been augmented using many different innovative molecular scaffolds. The synthesis of clustered ligands also facilitates fine-tuning of the spatial and topological proximities between the ligands, so as to allow the identification of optimal molecular features for significant binding affinity enhancements. The kinetic and thermodynamic parameters have been delineated in many instances, thereby allowing an ability to correlate the multivalent presentation and the observed ligand-receptor interaction profiles. This critical review presents various multivalent ligands, synthetic and semisynthetic, and mechanisms by which the weak binding affinities are overcome, and the ligand-receptor complexation leads to significantly enhanced binding affinities (157 references).

Kinetic characterization of rat brain type IIA sodium channel alpha-subunit stably expressed in a somatic cell line

1. The rat brain type IIA Na+ channel alpha-subunit was stably expressed in Chinese hamster ovary (CHO) cells. Current through the expressed Na+ channels was studied using the whole-cell configuration of the patch clamp technique. The transient Na+ current was sensitive to TTX and showed a bell-shaped peak current vs. membrane potential relation. 2. Na+ current inactivation was better described by the sum of two exponentials in the potential range -30 to +40 mV, with. a dominating fast component and a small slower component. 3. The steady-state inactivation, h(infinity), was related to potential by a Boltzmann distribution, underlying thr ee states of the inactivation gate. 4. Recovery of the channels from inactivation at different potentials in the range -70 to -120 mV were characterized by al? initial delay which decreased with hyperpolarization. The time course was well fitted by the sum of two exponentials. In this case the slower exponential was the major component, and both time constants decreased with hyperpolarization. 5. For a working description of the Na+ channel inactivation in this preparation, with a minimal deviation from the Hodgkin-Huxley model, a three-state scheme of the form O reversible arrow I-1 reversible arrow I-2 was proposed, replacing the original two-state scheme of the Hodgkin-Huxley model, and the rate constants are reported. 6. The instantaneous current-voltage relationship showed marked deviation from linearity and was satisfactorily fitted by the constant-field equation. 7. The time course of activation was described by an m(x) model. However, the best-fitted value of x varied with the membrane potential and had a mean value of 2. 8. Effective gating charge was determined to be 4.7e from the slope of the activation plot, plotted on a logarithmic scale. 9. The rate constants of activation, alpha(m) and beta(m), were determined. Their functional dependence on the membrane potential was investigated.

Topological close packed mu phase formation and the determination of diffusion parameters in the Co-Mo system

The study on the formation and growth of topological close packed (TCP) compounds is important to understand the performance of turbine blades in jet engine applications. These deleterious phases grow mainly by diffusion process in the superalloy substrate. Significant volume change was found because of growth of the p phase in Co-Mo system. Growth kinetics of this phase and different diffusion parameters, like interdiffusion, intrinsic and tracer diffusion coefficients are calculated. Further the activation energy, which provides an idea about the mechanism, is determined. Moreover, the interdiffusion coefficient in Co(Mo) solid solution and impurity diffusion coefficient of Mo in Co are determined.

Mutational analysis of active-site residues in the Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease: Asp(122) and Asp(193) are crucial to the double-stranded DNA cleavage activity whereas Asp(218) is not

Mycobacterium leprae recA harbors an in-frame insertion sequence that encodes an intein homing endonuclease (PI-MleI). Most inteins (intein endonucleases) possess two conserved LAGLIDADG (DOD) motifs at their ctive center. A common feature of LAGLIDADG-type homing endonucleases is that they recognize and cleave the same or very similar DNA sequences. However, PI-MleI is distinctive from other members of the family of LAGLIDADG-type HEases for its modular structure with functionally separable domains for DNA-binding and cleavage, each with distinct sequence preferences. Sequence alignment analyses of PI-MleI revealed three putative LAGLIDADG motifs; however, there is conflicting bioinformatics data in regard to their identity and specific location within the intein polypeptide. To resolve this conflict and to determine the active-site residues essential for DNA target site recognition and double-stranded DNA cleavage, we performed site-directed mutagenesis of presumptive catalytic residues in the LAGLIDADG motifs. Analysis of target DNA recognition and kinetic parameters of the wild-type PI-MleI and its variants disclosed that the two amino acid residues, Asp(122) (in Block C) and Asp(193) (in functional Block E), are crucial to the double-stranded DNA endonuclease activity, whereas Asp(218) (in pseudo-Block E) is not. However, despite the reduced catalytic activity, the PI-MleI variants, like the wild-type PI-MleI, generated a footprint of the same length around the insertion site. The D122T variant showed significantly reduced catalytic activity, and D122A and D193A mutations although failed to affect their DNA-binding affinities, but abolished the double-stranded DNA cleavage activity. On the other hand, D122C variant showed approximately twofold higher double-stranded DNA cleavage activity, compared with the wild-type PI-MleI. These results provide compelling evidence that Asp(122) and Asp(193) in DOD motif I and II, respectively, are bona fide active-site residues essential for DNA cleavage activity. The implications of these results are discussed in this report.

Aggregation of apolar peptides in organic solvents. Concentration dependence of 1H-nmr parameters for peptide NH groups in 310 helical decapeptide fragment of suzukacillin

Peptide NH chemical shifts and their temperature dependences have been monitored as a function of concentration for the decapeptide, Boc-Aib-Pro-Val-Aib-Val-Ala-Aib-Ala-Aib-Aib-OMe in CDCl3 (0.001-0.06M) and (CD3)2SO (0.001-0.03M). The chemical shifts and temperature coefficients for all nine NH groups show no significant concentration dependence in (CD3)2SO. Seven NH groups yield low values of temperature coefficients over the entire range, while one yields an intermediate value. In CDCl3, the Aib(1) NH group shows a large concentration dependence of both chemical shift and temperature coefficient, in contrast to the other eight NH groups. The data suggest that in (CD3)2SO, the peptide adopts a 310 helical conformation and is monomeric over the entire concentration range. In CDCl3, the 310 helical peptide associates at a concentration of 0.01M, with the Aib(1) NH involved in an intermolecular hydrogen bond. Association does not disrupt the intramolecular hydrogen-bonding pattern in the decapeptide.

A kinetic analysis of the tumor-associated galactopyranosyl-(1→3)-2-acetamido-2-deoxy-α-d-galactopyranoside antigen—lectin interaction

A kinetic study of the tumor-associated galactopyranosyl-(1→3)-2-acetamido-2-deoxy-α-d-galactopyranoside (T-antigen) with lectin peanut agglutinin is described. The disaccharide antigen was synthesized by chemical methods and was functionalized suitably for immobilization onto a carboxy-methylated sensor chip. The ligand immobilized surface was allowed interaction with the lectin peanut agglutinin, which acted as the analyte and the interaction was studied by the surface plasmon resonance method. The ligand—lectin interaction was characterized by the kinetic on-off rates and a bivalent analyte binding model was found to describe the observed kinetic constants. It was identified that the antigen-lectin interaction had a faster association rate constant (k a1) and a slower dissociation rate constant (k d1) in the initial binding step. The subsequent binding step showed much reduced kinetic rates. The antigen-lectin interaction was compared with the kinetic rates of the interaction of a galactopyranosyl-(1→4)-β-d-galactopyranoside derivative and a mannopyranoside derivative with the lectin.

Influence of roughness parameters and surface texture on friction during sliding of pure lead over 080 M40 steel

In the present investigation, tests were conducted on a tribological couple made of cylindrical lead pin with spherical tip against 080 M40 steel plates of different textures with varying roughness under both dry and lubricated conditions using an inclined pin-on-plate sliding tester. Surface roughness parameters of the steel plates were measured using optical profilometer. The morphologies of the worn surfaces of the pins and the formation of transfer layer on the counter surfaces were observed using a scanning electron microscope. It was observed that the coefficient of friction and the formation of transfer layer depend primarily on the surface texture of hard surfaces. A newly formulated non-dimensional hybrid roughness parameter called 'xi' (a product of number of peaks and maximum profile peak height) of the tool surface plays an important role in determining the frictional behaviour of the surfaces studied. The effect of surfaces texture on coefficient of friction was attributed to the variation of plowing component of friction, which in turn depends on the roughness parameter 'xi'.

Comparison of performance parameters of poly(3,4 ethylenedioxythiophene) (PEDOT) based electrochromic device on glass with and without counter electrode

Conjugated polymers are promising materials for electrochromic device technology. Aqueous dispersions of poly(3,4-ethylenedioxythiophene)-(PEDOT) were spin coated onto transparent conducting oxide (TCO) coated glass substrates. A seven-layer electrochromic device was fabricated with the following configuration: glass/transparent conducting oxide (TCO)/PEDOT (main electrochromic layer)/gel electrolyte/prussian blue (counter electrode)/TCO/glass. The device fabricated with counter electrode (Prussian blue) showed a contrast of 18% and without counter electrode showed visible contrast of 5% at 632 nm at a voltage of 1.9 V. The comparison of the device is done in terms of the colouration efficiency of the devices with and without counter electrode.

Characterization of hot deformation behavior of Zr-1Nb-1Sn alloy

The hot deformation behavior of beta-quenched Zr-1 Nb-1Sn was studied in the temperature range 650-1050 degrees C and strain rate range 0.001-100 s(-1) using processing maps. These maps revealed three different domains: a domain of dynamic recovery at temperatures <700 degrees C and at strain rates <3 x 10(-3) s(-1), a domain of dynamic recrystallization in the temperature range 750-950 C-degrees and at strain rates <10(-2) S-1 with a peak at 910 degrees C and 10(-3) S-1 (in alpha + beta phase field), and a domain of large-grain superplasticity in the beta phase field at strain rates <10(-2) s(-1). In order to identify the rate controlling mechanisms involved in these domains, kinetic analysis was carried out to determine the various activation parameters. In addition, the processing maps showed a regime of flow instability spanning both alpha + beta and beta phase fields. The hot deformation behavior of Zr 1Nb-1Sn was compared with that of Zr, Zr-2.5Nb and Zircaloy-2 to bring out the effects of alloy additions. (C) 2006 Elsevier BN. All rights reserved.

Gaussian mixture model based switched split vector quantization of LSF parameters

We address the issue of rate-distortion (R/D) performance optimality of the recently proposed switched split vector quantization (SSVQ) method. The distribution of the source is modeled using Gaussian mixture density and thus, the non-parametric SSVQ is analyzed in a parametric model based framework for achieving optimum R/D performance. Using high rate quantization theory, we derive the optimum bit allocation formulae for the intra-cluster split vector quantizer (SVQ) and the inter-cluster switching. For the wide-band speech line spectrum frequency (LSF) parameter quantization, it is shown that the Gaussian mixture model (GMM) based parametric SSVQ method provides 1 bit/vector advantage over the non-parametric SSVQ method.

Computationally efficient optimum weighting function for vector quantization of LSF parameters

We propose a new weighting function which is computationally simple and an approximation to the theoretically derived optimum weighting function shown in the literature. The proposed weighting function is perceptually motivated and provides improved vector quantization performance compared to several weighting functions proposed so far, for line spectrum frequency (LSF) parameter quantization of both clean and noisy speech data.

Reactive Pulsed Laser Deposition of titanium nitride thin film: Optimization of process parameters using Secondary Ion Mass Spectrometry

Reactive Pulsed Laser Deposition is a single step process wherein the ablated elemental metal reacts with a low pressure ambient gas to form a compound. We report here a Secondary Ion Mass Spectrometry based analytical methodology to conduct minimum number of experiments to arrive at optimal process parameters to obtain high quality TiN thin film. Quality of these films was confirmed by electron microscopic analysis. This methodology can be extended for optimization of other process parameters and materials. (C) 2009 Elsevier B.V. All rights reserved.

Influence of surface texture and roughness parameters on friction and transfer layer formation during sliding of aluminium pin on steel plate

Surface texture of harder mating surfaces plays an important role during sliding against softer materials and hence the importance of characterizing the surfaces in terms of roughness parameters. In the present investigation, basic studies were conducted using inclined pin-on-plate sliding tester to understand the surface texture effect of hard surfaces on coefficient of friction and transfer layer formation. A tribological couple made of a super purity aluminium pin against steel plate was used in the tests. Two surface parameters of steel plates, namely roughness and texture, were varied in the tests. It was observed that the transfer layer formation and the coefficient of friction along with its two components, namely, the adhesion and plowing, are controlled by the surface texture and are independent of surface roughness (R-a). Among the various surface roughness parameters, the average or the mean slope of the profile was found to explain the variations best. Under lubricated conditions, stick-slip phenomena was observed, the amplitude of which depends on the plowing component of friction. The presence of stick-slip motion under lubricated conditions could be attributed to the molecular deformation of the lubricant component confined between asperities. (C) 2009 Elsevier B. V. All rights reserved.

Numerical studies on channel formation and growth during solidification: Effect of process parameters

In the present work, solidification of a hyper-eutectic ammonium chloride solution in a bottom-cooled cavity (i.e. with stable thermal gradient) is numerically studied. A Rayleigh number based criterion is developed, which determines the conditions favorable for freckles formation. This criterion, when expressed in terms of physical properties and process parameters, yields the condition for plume formation as a function of concentration, liquid fraction, permeability, growth rate of a mushy layer and thermophysical properties. Subsequently, numerical simulations are performed for cases with initial and boundary conditions favoring freckle formation. The effects of parameters, such as cooling rate and initial concentration, on the formation and growth of freckles are investigated. It was found that a high cooling rate produced larger and more defined channels which are retained for a longer durations. Similarly, a lower initial concentration of solute resulted in fewer but more pronounced channels. The number and size of channels are also found to be related to the mushy zone thickness. The trends predicted with regard to the variation of number of channels with time under different process conditions are in accordance with the experimental observations reported in the literature.