Analysis of human chorionic gonadotropin-monoclonal antibody interaction in BIAcore

Kinetic studies of macromolecular ligand-ligate interaction have generated ample interest since the advent of plasmon resonance based instruments like BIAcore. Most of the studies reported in literature assume a simple 1 : 1 Langmuir binding and complete reversibility of the system. However we observed that in a high affinity antigen-antibody system [human chorionic gonadotropin-monoclonal antibody (hCG-mAb)] dissociation is insignificant and the sensogram data cannot be used to measure the equilibrium and kinetic parameters. At low concentrations of mAb the complete sensogram could be fitted to a single exponential. Interestingly we found that at higher mAb concentrations, the binding data did not conform to a simple bimolecular model. Instead, the data fitted a two-step model, which may be because of surface heterogeneity of affinity sites. In this paper, we report on the global fit of the sensograms. We have developed a method by which a single two-minute sensogram can be used in high affinity systems to measure the association rate constant of the reaction and the functional capacity of the ligand (hCG) immobilized on the chip. We provide a rational explanation for the discrepancies generally observed in most of the BIAcore sensograms

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.

Analysis of dynamics and mechanism of ligand binding to Artocarpus integrifolia agglutinin. A 13C and 19F NMR study

Binding of 13C-labeled N-acetylgalactosamine (13C-GalNAc) and N-trifluoroacetylgalactosamine (19F-GalNAc) to Artocarpus integrifolia agglutinin has been studied using 13C and 19F nuclear magnetic resonance spectroscopy, respectively. Binding of these saccharides resulted in broadening of the resonances, and no change in chemical shift was observed, suggesting that the alpha- and beta-anomers of 13C-GalNAc and 19F-GalNAc experience a magnetically equivalent environment in the lectin combining site. The alpha- and beta-anomers of 13C-GalNAc and 19F-GalNAc were found to be in slow exchange between free and protein bound states. Binding of 13C-GalNAc was studied as a function of temperature. From the temperature dependence of the line broadening, the thermodynamic and kinetic parameters were evaluated. The association rate constants obtained for the alpha-anomers of 13C-GalNAc and 19F-GalNAc (k+1 = 1.01 x 10(5) M-1.s-1 and 0.698 x 10(5) M-1.s-1, respectively) are in close agreement with those obtained for the corresponding beta-anomers (k+1 = 0.95 x 10(5) M-1.s-1 and 0.65 x 10(5) M-1.s-1, respectively), suggesting that the two anomers bind to the lectin by a similar mechanism. In addition these values are several orders of magnitude slower than those obtained for diffusion controlled processes. The dissociation rate constants obtained are 49.9, 56.9, 42, and 43 s-1, respectively, for the alpha- and beta-anomers of 13C-GalNAc and 19F-GalNAc. A two-step mechanism has been proposed for the interaction of 13C-GalNAc and 19F-GalNAc with A. integrifolia lectin in view of the slow association rates and high activation entropies. The thermodynamic parameters obtained for the association and dissociation reactions suggest that the binding process is entropically favored and that there is a small enthalpic contribution.

Kinetic theory for the density plateau in the granular flow down an inclined plane

The striking lack of observable variation of the volume fraction with height in the center of a granular flow down an inclined plane is analysed using constitutive relations obtained from kinetic theory. It is shown that the rate of conduction in the granular energy balance equation is O(delta(2)) smaller than the rate of production of energy due to mean shear and the rate of dissipation due to inelastic collisions, where the small parameter delta = (d/(1 - e(n))H-1/2), d is the particle diameter, en is the normal coefficient of restitution and H is the thickness of the flowing layer. This implies that the volume fraction is a constant in the leading approximation in an asymptotic analysis in small delta. Numerical estimates of both the parameter delta and its pre-factor are obtained to show that the lack of observable variation of the volume fraction with height can be explained by constitutive relations obtained from kinetic theory.

A kinetic investigation of thermal degradation of poly(vinyl formals)

Several samples of poly(vinyl formal) having the same vinyl alcohol content (8–9%) but varying contents of vinyl acetate (6–22%) and vinyl formol (70–85%) were prepared and subjected to thermogravimetric analysis, in air and nitrogen atmospheres, employing both isothermal and dynamic methods. Kinetic parameters determined from both the isothermal and dynamic TGA data are compared. The activation energy is seen to be largely dependent on the degree of conversion, implying a complex degradation reaction. The activation energy is also much less for degradation in air than in nitrogen, which can be explained by a reaction with oxygen-producing structures favoring degradation. The activation energy is less sensitive to variation in polymer composition for degradation in air than in nitrogen. Thus, in the dynamic process, the activation energy value decreases (from 36 to 23 kcal/mole) with increasing acetate content (from 6 to 22%) in nitrogen atmosphere, while in air the activation energy value increases only moderately (from 21 to 27 kcal/mole) with increasing acetate content (from 6 to 22%). The order of reaction is nearly unity, irrespective of the composition of the polymer, both in air and nitrogen.

A kinetic investigation of thermal degradation of poly(vinyl formals)

Several samples of poly(vinyl formal) having the same vinyl alcohol content (8–9%) but varying contents of vinyl acetate (6–22%) and vinyl formol (70–85%) were prepared and subjected to thermogravimetric analysis, in air and nitrogen atmospheres, employing both isothermal and dynamic methods. Kinetic parameters determined from both the isothermal and dynamic TGA data are compared. The activation energy is seen to be largely dependent on the degree of conversion, implying a complex degradation reaction. The activation energy is also much less for degradation in air than in nitrogen, which can be explained by a reaction with oxygen-producing structures favoring degradation. The activation energy is less sensitive to variation in polymer composition for degradation in air than in nitrogen. Thus, in the dynamic process, the activation energy value decreases (from 36 to 23 kcal/mole) with increasing acetate content (from 6 to 22%) in nitrogen atmosphere, while in air the activation energy value increases only moderately (from 21 to 27 kcal/mole) with increasing acetate content (from 6 to 22%). The order of reaction is nearly unity, irrespective of the composition of the polymer, both in air and nitrogen.

Kinetic evolution studies of silver nanoparticles in a bio-based green synthesis process

Silver nanoparticles are being extensively studied due to their widespread applications and unique properties. In the present study, the growth kinetics of silver nanoparticles as synthesized on reduction of silver nitrate solution by aqueous extract of Azadirachta indica leaves was investigated. The formation of silver nanoparticles was preliminarily monitored by measuring the absorption maxima at different time intervals after adding the reducing agent to the silver salt solution (0.5, 1, 1.5, 2, 2.5, 3, 3.5 and 4 h). At different time points characterization studies were conducted using X-ray diffraction studies, FT-IR techniques, zeta potential studies and transmission electron microscopy. The total available silver in the reaction medium was determined at different durations using ICP-OES. The changes in reduction potential in the medium were also monitored using potentiometric analysis. The results confirm a definite change in the medium pertaining to formation of the stable nanoparticles after 2 h, and a significant increase in the agglomeration tendency after 4 h of interaction. The growth kinetic data of the nanoparticles till 3.5 h was found to fit the LSW model confirming diffusion limited growth. (C) 2011 Elsevier B.V. All rights reserved.

The gasification of wood-char spheres in CO2---N2 mixtures: analysis and experiments

The gasification of charcoal spheres in an atmosphere of carbon-dioxide-nitrogen mixture involving diffusion and reactions in the pores is modelled and the results are compared with experiments of Standish and Tanjung and those performed in the laboratory on wood-char spheres to determine the effects of diameter, density, gas composition and flow. The results indicate that the conversion time, t(c) approximately d1.03 for large particles (> 5 mm), departing substantially from the t(c) approximately d2 law valid for diffusion limited conditions. The computational studies indicate that the kinetic limit for the particle is below 100 mum. The conversion time varies inversely as the initial char density as expected in the model. Predictions from the model show that there is no significant change in conversion time up to 60% N2 consistent with the CO2-N2 experiments. The variation of diameter and density with time are predicted. The peculiar dependence of conversion time on flow velocity in the experiments is sought to be explained by opposing free and forced convection heat transfer and the attempt is only partly successful. The studies also indicate that the dependence on the CO concentration with low CO2 is significant, indicating the need for multistep reaction mechanism against the generally accepted single-step reaction.

Interaction of sheep liver apo-serine hydroxymethyltransferase with pyridoxal-5'-phosphate: A physicochemical, kinetic, and thermodynamic study

Sheep liver serine hydroxymethyltransferase (EC 2.1.2.1) is a homotetramer of M(r) 213,000 requiring pyridoxal-5'-phosphate (PLP) as cofactor, Removal of PLP from the holoenzyme converted the enzyme to the apo form which, in addition to being inactive, was devoid of the characteristic absorption spectrum. Upon the addition of PLP to the apoenzyme, complete activity was restored and the visible absorption spectrum with a maximum at 425 nm was regained. The interaction of PLP with the apoenzyme revealed two phases of reaction with pseudo-first-order rate constants of 20 +/- 5 s(-1) and 12.2 +/- 2.0 x 10(-3) s(-1), respectively. However, addition of PLP to the apoenzyme did not cause gross conformational changes as evidenced by circular dichroic and fluorescence spectroscopy. Although conformationally apoenzyme and holoenzyme were indistinguishable, they had distinct apparent melting temperatures of 51 +/- 2 and 58 +/- 2 degrees C, respectively, and the reconstituted holoenzyme was thermally as stable as the native holoenzyme. These results suggested that there was no apparent difference in the secondary structure of holoenzyme, apoenzyme, and reconstituted holoenzyme, However, sedimentation analysis of the apoenzyme revealed the presence of two peaks of S-20,S-w values of 8.7 +/- 0.5 and 5.7 +/- 0.3 S, respectively. A similar pattern was observed when the apoenzyme was chromatographed on a calibrated Sephadex G-150 column. The first peak corresponded to the tetrameric form (M(r) 200,000 +/- 15,000) while the second peak had a M(r) of 130,000 +/- 10,000. Reconstitution experiments revealed that only the tetrameric form of the apoenzyme could be converted into an active holoenzyme while the dimeric form could not be reconstituted into an active enzyme. These results demonstrate that PLP plays an important role in maintaining the structural integrity of the enzyme by preventing the dissociation of the enzyme into subunits, in addition to its function in catalysis. (C) 1996 Academic Press, Inc.

A kinetic study of the phase transformations in Al2O3 and Na2O · 6Al2O3 by a combined use of 27Al MAS NMR spectroscopy and x-ray diffraction: Importance of nucleation

Phase transformations of Al2O3 and Na2O · 6Al2O3 prepared by the gel route have been investigated for the first time by 27Al MAS NMR spectroscopy in combination with x-ray diffraction. Of particular interest in the study is the kinetics of the γ → α and γ → β transformations, respectively, in these two systems. Analysis of the kinetic data shows the important role of nucleation in both these transformations.

Analysis of a cascade‐pumped 16 μm CO2‐N2 downstream‐mixing gasdynamic laser

The generation of a 16 μm laser beam through cascading in a downstream‐mixing CO2 gasdynamic laser is studied. To simulate actual lasing action, a generalized, two‐dimensional, flow‐radiation‐coupled power extraction model for a gasdynamic laser is used. Also, to model the cascade process a new four‐mode CO2‐N2 vibrational kinetic model has been proposed. The steady‐state intensity obtained for an exclusive 9.4 μm transition is of the order of 5×107 W/m2. In the cascade mode of operation the steady‐state intensities for 9.4 and 16 μm transitions of the order of 5×107 W/m2 and 1.0×106 W/m2, respectively, have been obtained.

Directional grain growth from anisotropic kinetic roughening of grain boundaries in sheared colloidal crystals

The fabrication of functional materials via grain growth engineering implicitly relies on altering the mobilities of grain boundaries (GBs) by applying external fields. Although computer simulations have alluded to kinetic roughening as a potential mechanism for modifying GB mobilities, its implications for grain growth have remained largely unexplored owing to difficulties in bridging the widely separated length and time scales. Here, by imaging GB particle dynamics as well as grain network evolution under shear, we present direct evidence for kinetic roughening of GBs and unravel its connection to grain growth in driven colloidal polycrystals. The capillary fluctuation method allows us to quantitatively extract shear-dependent effective mobilities. Remarkably, our experiments reveal that for sufficiently large strains, GBs with normals parallel to shear undergo preferential kinetic roughening, resulting in anisotropic enhancement of effective mobilities and hence directional grain growth. Single-particle level analysis shows that the mobility anisotropy emerges from strain-induced directional enhancement of activated particle hops normal to the GB plane. We expect our results to influence materials fabrication strategies for atomic and block copolymeric polycrystals as well.

Charge Density Analysis of Ferulic Acid: Robustness of a Trifurcated C-H center dot center dot center dot O Hydrogen Bond

The toplogical features of a sporadic trifurcated C-H center dot center dot center dot O interaction region, where an oxygen atom acts as an acceptor of three weak hydrogen bonds, has been investigated by experimental and theoretical charge density analysis of ferulic acid. The interaction energy of the asymmetric molecular dimer formed by the trifurcated C-H center dot center dot center dot O motif, based on the multipolar model, is shown to be greater than the corresponding asymmetric O-H center dot center dot center dot O dimer in this crystal structure. Further, the hydrogen bond energies associated with these interaction motifs have been estimated from the local kinetic and potential energy densities at the bond critical points. The trends suggest that the interaction energy of the trifurcated C-H center dot center dot center dot O region is comparable to that of a single O-H center dot center dot center dot O hydrogen bond.

Activation of Fly Ash–Lime Reactions: Kinetic Approach

Lime–fly ash reactions play a key role in improving the mechanical strength and tailoring the permeability characteristics of compacted fly ash. Activation of fly ash–lime pozzolanic reactions should accelerate the rate of strength development and possibly mobilize higher compressive strengths, facilitating improved engineering performance of fly ash amended materials. This paper makes an assessment of activation of lime–fly ash reactions by curing compacted fly ash–lime specimens at ambient (25°C) and at elevated temperature (80°C). The kinetics of fly ash–lime reactions are examined by monitoring the reacted lime as a function of curing period and temperature. The influence of variations in fly ash/lime content and dry density on the compressive strength developed by specimens at both temperatures is evaluated. The thermodynamic parameters for the fly ash–lime reactions have also been examined. Experimental results showed that curing at 80°C for 24 h accelerated fly ash–lime reactions such that it caused the steam cured (SC) specimens to evelop 1.21–2.44 fold larger strengths than room-temperature cured (RTC) specimens cured at 25°C for 28 days. Analysis of thermodynamic parameters indicated that the fly ash–lime reactions are thermodynamically favored at fly ash contents of 50–70% and lime additions of 16–20%, and the reactions are endothermic in nature. DOI: 10.1061/(ASCE)MT.1943-5533.0000482. © 2012 American Society of Civil Engineers.

Kinetics of CO oxidation on palladium using microkinetics coupled with reaction route analysis

A plausible microkinetic model has been proposed for the CO oxidation reaction catalysed by palladium (Pd) with the kinetic parameters obtained from the literature. A robust rate expression using the reaction route analysis has been developed for the presented microkinetic scheme and the obtained rate expressions have been validated against the experimental data presented in the literature. A wide range of experimental conditions ranging from single Pd crystals under ultra-high vacuum conditions and impregnated Pd used for fixed bed experiments under atmospheric pressure has been used to validate the reaction mechanism. (C) 2015 Elsevier Ltd. All rights reserved.