Interaction of malachite green with bovine serum albumin: determination of the binding mechanism and binding site by spectroscopic methods

The interaction between malachite green (MG) and bovine serum albumin (BSA) under simulative physiological conditions was investigated by the methods of fluorescence spectroscopy, UV-vis absorption and circular dichroism (CD) spectroscopy. Fluorescence data showed that the fluorescence quenching of BSA by MG was the result of the formation of the MG-BSA complex. According to the modified Stern-Volmer equation, the effective quenching constants (K(a)) between MG and BSA at four different temperatures were obtained to be 3.734 x 10(4), 3.264 x 10(4), 2.718 x 10(4), and 2.164 x 10(4)L mol(-1), respectively. The enthalpy change (Delta H) and entropy change (DeltaS) were calculated to be -27.25 kJ mol(-1) and -11.23 J mol(-1)K(-1), indicating that van der Waals force and hydrogen bonds were the dominant intermolecular force in stabilizing the complex. Site marker competitive experiments indicated that the binding of MG to BSA primarily took place in sub-domain IIA. The binding distance (r) between MG and the tryptophan residue of BSA was obtained to be 4.79 nm according to F?rster theory of non-radioactive energy transfer. The conformational investigation showed that the presence of MG decreased the alpha-helical content of BSA (from 62.6% to 55.6%) and induced the slight unfolding of the polypeptides of protein, which confirmed some micro-environmental and conformational changes of BSA molecules.     

A spectroscopic study on the interaction between gold nanoparticles and hemoglobin

The interaction between horse hemoglobin and gold nanoparticles was studied using optical spectroscopy. UV-vis and fluorescence spectra show that a spontaneous binding process occurred between hemoglobin and gold nanoparticles. The Soret band of hemoglobin in the presence of gold nanoparticles does not show significant changes, which proves that the protein retained its biological function. A shift to longer wavelengths appears in the plasmonic band of gold nanoparticles upon the attachment of hemoglobin molecules. Gold nanoparticles quench the fluorescence emission of tryptophan residues in the structure of hemoglobin. The Stern-Volmer quenching constant, the binding constant and the number of binding sites were also calculated. Thermodynamic parameters indicate that the binding was mainly due to hydrophobic interactions.     

Empirical modeling methods using partial data

Methods were developed to calculate empirical models for device error behavior from data sets with missing data. These models can be used to develop reduced test point testing procedures for the devices. Normally, models are built from only full data measurement sets, and partial data sets are discarded. For models built from noisy data, the accuracy of the models improves as more data is used. This paper explores methods to use partial data sets. Both real and simulated data results are described. Simulations show that the proposed partial data methods improve the accuracy of the models for some test points. When these methods are applied to real data where the underlying model has changed, the improvement is less than the simulations predict.     

The interaction between 4-aminoantipyrine and bovine serum albumin: multiple spectroscopic and molecular docking investigations

4-Aminoantipyrine (AAP) is widely used in the pharmaceutical industry, in biochemical experiments and in environmental monitoring. AAP as an aromatic pollutant in the environment poses a great threat to human health. To evaluate the toxicity of AAP at the protein level, the effects of AAP on bovine serum albumin (BSA) were investigated by multiple spectroscopic techniques and molecular modeling. After the inner filter effect was eliminated, the experimental results showed that AAP effectively quenched the intrinsic fluorescence of BSA via static quenching. The number of binding sites, the binding constant, the thermodynamic parameters and binding subdomain were measured, and indicated that AAP could spontaneously bind with BSA on subdomain IIIA through electrostatic forces. Molecular docking results revealed that AAP interacted with the Glu 488 and Glu 502 residues of BSA. Furthermore, the conformation of BSA was demonstrably changed in the presence of AAP. The skeletal structure of BSA loosened, exposing internal hydrophobic aromatic ring amino acids and peptide strands to the solution.     

Surrogate modeling of multiscale models using kernel methods

This work investigates the possibilities of acceleration and approximation of multiscale systems using kernel methods. The key element is to learn the interface between the different scales using a fast surrogate for the microscale model, which is given by multivariate kernel expansions. The expansions are computed using statistically representative samples of input and output of the microscale model. We apply both support vector machines and a vectorial kernel greedy algorithm as learning methods. We demonstrate the applicability of the resulting surrogate models using two multiscale models from different engineering disciplines. We consider, first, a human spine model coupling a macroscale multibody system with a microscale intervertebral spine disc model and, second, a model for simulation of saturation overshoots in porous media involving nonclassical shock waves. Copyright © 2014 John Wiley & Sons, Ltd.     

Investigation of electrolyte measurement in diluted whole blood using spectroscopic and chemometric methods

The feasibility of using near-infrared (NIR) spectroscopy in combination with partial least-squares (PLS) regression was explored to measure electrolyte concentration in whole blood samples. Spectra were collected from diluted blood samples containing randomized, clinically relevant concentrations of Na+, K+, and Ca2+. Sodium was also studied in lysed blood. Reference measurements were made from the same samples using a standard clinical chemistry instrument. Partial least squares (PLS) was used to develop calibration models for each ion with acceptable results (Na+, R2 = 0.86, CVSEP = 9.5 mmol/L; K+, R2 = 0.54, CVSEP = 1.4 mmol/L; Ca2+, R2 = 0.56, CVSEP = 0.18 mmol/L). Slightly improved results were obtained using a narrower wavelength region (470-925 nm) where hemoglobin, but not water, absorbed indicating that ionic interaction with hemoglobin is as effective as water in causing measurable spectral variation. Good models were also achieved for sodium in lysed blood, illustrating that cell swelling, which is correlated with sodium concentration, is not required for calibration model development.     

Insights into the binding of 2-aminobenzothiazole with human serum albumin (HSA): spectroscopic investigation and molecular modeling studies

As one of the important thiazole derivatives, 2-aminobenzothiazole (2-ABT) has been widely used as a structural unit in the synthesis of anti-oxidants, anti-inflammatories, herbicides, antibiotics, and thermoplastic polymers. In this study, the interaction of 2-ABT with human serum albumin (HSA) was investigated in vitro under simulated physiological conditions, using multi-spectroscopic techniques and a molecular modeling study. The binding constant and binding sites were determined through fluorescence quenching spectra. The site-competitive replacement experiments revealed that the precise binding site of 2-ABT on HSA was site II (subdomain IIIA). Moreover, molecular docking results illustrated the electrostatic interaction between Glu 450 and 2-ABT, in accordance with the conclusions from the calculated thermodynamic parameters and the effect of ionic strength. The effect of 2-ABT on the conformational changes of HSA were evaluated by ultraviolet-visible (UV-Vis) absorption, three-dimensional (3D) fluorescence, synchronous fluorescence, and circular dichroism (CD) spectroscopy. This work facilitates comprehensive understanding of the binding of 2-ABT with HSA, contributing to evaluate the molecular transportation mechanism and biotoxicity of 2-aminobenzothiazole derivatives in vivo.     

N-terminal adducts of bovine hemoglobin with glutaraldehyde in a hemoglobin-based oxygen carrier

Hemoglobin-based oxygen carriers (HBOCs) are being developed for the medical field, but because they could increase an athlete's performance, they are misapplied for doping purposes. We previously presented a screening method to detect Oxyglobin (Biopure Corp.) and PolyHeme (Northfield Laboratories Inc.) in serum samples using total acid hydrolysis followed by electrospray mass spectrometry analyses. An alternative mass spectrometric method involving enzymatic hydrolysis is here presented. Digestion of Oxyglobin by endoproteinase Glu-C and LC/MS analyses of the mixture allowed the detection of unique peptidic fragments in comparison with a bovine hemoglobin digest. Tandem mass spectrometry experiments of these peptide ions were performed, and two specific species were actually identified as the N-terminal enzymatic fragment of the beta chain carrying two different modifications. Sequential MS3 experiments using an ion trap mass spectrometer permitted us to locate the chemical modification by the glutaraldehyde on the NH2-terminal group and to propose a structure for the modified peptides. In another set of experiments, screening of these two diagnostic ions into Oxyglobin-spiked serums using precursor ion scan mode in a triple quadrupole instrument allowed the detection of this HBOC with a detection limit of 2 g L(-1).     

Determination of first-order molecular hyperpolarizability of EAADCy and EDMAADCy using steady-state spectroscopic data and quantum-chemical calculations

Ethyl 5-(4-aminophenyl)-3-amino-2,4-dicyanobenzoate (EAADCy) and ethyl 5-(4-dimethylaminophenyl)-3-amino-2,4-dicyanobenzoate (EDMAADCy) organic molecules containing separate electron donor and electron acceptor groups belong to biphenyl derivatives in which a large dipole moment change between ground (S₀) and the first intramolecular charge transfer excited (S₁) states, as well as a large transition moment have been noted. The existence of electronically excited states with a strong intermolecular charge transfer (ICT) character is an essential prerequisite for large non-linear optical properties. Therefore, in this paper, we present a scrupulous analysis of the first-order hyperpolarizabilities of the studied molecules using an equivalent internal field model of an organic molecule. The calculated (using semiempirical calculations, CAChe WS 5.04) additive part of the first-order hyperpolarizability, β_add, values are discussed in relationship to the experimental data of the charge transfer hyperpolarizability, β_CT, obtained from steady-state spectroscopic measurements.     

Comprehensive structural studies of ultra-fine nanocrystalline calcium hydroxyapatite using MAS NMR and FT-IR spectroscopic methods

Three nanoapatites produced using a microwave solvothermal synthesis (MSS), including one with a mean crystal size of only 6 nm, were characterized by high-resolution solid-state NMR (¹H and ³¹P) and FT-IR spectroscopies. It was found that nanoapatite particles had an inner crystal core covered by a non-apatitic surface hydrated layer with an outermost liquid-like zone. Various physicochemical properties of those apatite compartments were determined. Important structural details, such as deficiency and disorder of structural OH⁻ ions were discovered and discussed. The materials were also compared with respect to the reaction time and thermal post-synthesis treatment in order to optimize their preparation conditions to the required performance. The study emphasizes the influence of the surface hydrated layer on the physicochemical properties and biological activity of nanoapatites.     

Interaction of molecular and atomic hydrogen with single-wall carbon nanotubes

Density functional calculations are performed to study the interaction of molecular and atomic hydrogen with (5,5) and (6,6) single-wall carbon nanotubes. Molecular physisorption is predicted to be the most stable adsorption state, with the molecule at equilibrium at a distance of 5-6 a.u. from the nanotube wall. The physisorption energies outside the nanotubes are approximately 0.07 eV, and larger inside, reaching a value of 0.17 eV inside the (5,5) nanotube. Although these binding energies appear to be lower than the values required for an efficient adsorption/desorption operation at room temperature and normal pressures, the expectations are better for operation at lower temperatures and higher pressures, as found in many experimental studies. A chemisorption state with the molecule dissociated has also been found, with the H atoms much closer to the nanotube wall. However, this state is separated from the physisorption state by an activation barrier of 2 eV or more. The dissociative chemisorption weakens carbon-carbon bonds, and the concerted effect of many incoming molecules with sufficient kinetic energies can lead to the scission of the nanotube.     

Crystal growth study using combination of molecular dynamics and Monte Carlo methods

Molecular dynamics method although provides details of energies of the system as a function of time, is not suited to simulate the processes involving activation processes. Therefore, we attempted to combine the molecular dynamics and Monte Carlo methods. Using molecular dynamics, the energies of the system were calculated which were subsequently combined with Monte Carlo method using random numbers, epitaxial growth of (111) plane of copper, silver, and gold. While surface adsorption and surface diffusion for copper, silver, and gold were simulated by use of molecular dynamics method, the relation between the growth rate of thin films and the packing density of atoms were obtained using Monte Carlo simulation. Thus, by combining the results of the molecular dynamics method and the Monte Carlo method the growth process of thin films at elevated temperatures were obtained, which is too tedious to be calculated by molecular dynamics alone.     

Relative contributions of hemoglobin and myoglobin to near-infrared spectroscopic images of cardiac tissue

Near-infrared (NIR) spectroscopic imaging is emerging as a unique tool for intra-operative assessment of myocardial oxygenation, but quantitative interpretation of the images is not straightforward. One confounding factor specific to muscle tissue (both skeletal and cardiac) is that the visible/NIR absorbance spectrum of myoglobin (Mb), an intracellular O(2) storage protein, is virtually identical to that of hemoglobin (Hb). As a consequence, the relative contributions of Mb and Hb to the NIR spectra measured in vivo for blood perfused muscle tissue cannot be determined from the measured spectra alone. To estimate the relative contributions of Mb and Hb to NIR spectra and spectroscopic images, isolated pig hearts were perfused first with a Hb-free blood substitute (Krebs-Henseleit buffer; KHB) and then with a 50/50 KHB/blood mixture, with spectroscopic images acquired at each step. Tissue Mb levels were estimated directly from the measurements during KHB perfusion, and total (Mb+Hb) levels were estimated from the images acquired during 50/50 blood/KHB perfusion. Myoglobin accounted for 63 +/- 11% of the total heme content during perfusion with the 50/50 mixture (implying that Mb would contribute 46% of the combined (Mb+Hb) NIR profile during whole blood perfusion), confirming that Mb contributes substantially to near-infrared absorbance spectra of blood perfused cardiac tissue.     

Multiscale modeling of fluid transport in heterogeneous materials using discrete Boltzmann methods

The lattice Boltzmann method is a promising approach for modeling single and multicomponent fluid flow in complex geometries like porous materials. Here, we review some of our previous work and discuss some recent developments concerning fluid flow in multiple pore size materials. After presenting some simple test cases to validate the model, results from large scale simulations of single and multi-component fluid flow through digitized Fontainebleau sandstone, generated by X-Ray microtomography, are given. Reasonably good agreement was found when compared to experimentally determined values of permeability for similar rocks. Finally, modification of the lattice Boltzmann equations, to describe flow in microporous materials, is described. The potential for modeling flows in other microstructures of interest to concrete technology will be discussed.

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Résumé La méthode Lattice Boltzmann est une approche à grand potentiel pour modeler l'écoulement à travers une géométrie complexe, comme celle des matériaux poreux, d'un fluide simple ou à composants multiples. Ici, nous passerons en revue une partie du travail complété et nous discuterons les développements récents concernant l'écoulement d'un fluide dans un matériau poreux ayant une large distribution de la dimension des pores. Nous présenterons, d'abord, des cas simples pour valider le modèle et, ensuite, des cas plus complexes incluant des écoulements de fluides simples ou à composants multiples dans une structure digitalisée d'un grès de Fontainebleau. La structure du grès fut générée par micrographie à Rayon-X. Les résultats du modèle ont une bonne corrélation avec la mesure de perméabilité déterminée sur des pierres similaires. Enfin, une modification des équations de la lattice Boltzmann permet de décrire l'écoulement à travers un matériau micro-poreux. Nous discuterons aussi la possibilité de modeler l'écoulement d'un fluide à travers d'autres micro-structures inspirées de la technologie du béton.

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Editorial Note The National Institute of Standards and Technology (NIST) is a RILEM Titular Member.     

Computational modeling of mixed-mode fatigue crack growth using extended finite element methods

The extended finite element method (XFEM) combined with a cyclic cohesive zone model (CCZM) is discussed and implemented for analysis of fatigue crack propagation under mixed-mode loading conditions. Fatigue damage in elastic-plastic materials is described by a damage evolution equation in the cohesive zone model. Both the computational implementation and the CCZM are investigated based on the modified boundary layer formulation under mixed-mode loading conditions. Computational results confirm that the maximum principal stress criterion gives accurate predictions of crack direction in comparison with known experiments. Further popular multi-axial fatigue criteria are compared and discussed. Computations show that the Findley criterion agrees with tensile stress dominant failure and deviates from experiments for shear failure. Furthermore, the crack propagation rate under mixed mode loading has been investigated systematically. It is confirmed that the CCZM can agree with experiments.     

Probabilistic modeling of chloride-induced corrosion in concrete structures using first- and second-order reliability methods

Concrete structures are subjected to chloride-induced corrosion that can lead to shortened service life. Reliable predictions of life cycle performance of concrete structures are critical to the optimization of their life cycle design and maintenance to minimize their life cycle costs. This paper presents two simplified semi-analytical probabilistic models based on the first- and second-order reliability methods to model the uncertainty of the key parameters including surface chloride concentration, chloride threshold, cover depth and diffusion coefficient, which govern the chloride ingress into concrete and corrosion of reinforcing steel. A case study of a reinforced concrete highway bridge deck is used to illustrate the capability and efficiency of these simplified probabilistic models in modeling the uncertainty and predicting the time-dependent probability of corrosion. The models enable to quantify the impact of the different governing parameters on probability of corrosion and service life, which can be used to develop cost-effective management strategies.     

Structural and functional characterization of glutaraldehyde-polymerized bovine hemoglobin and its isolated fractions

Glutaraldehyde-polymerized bovine hemoglobin (PolyHbBv, trade name Oxyglobin), is a non-site-specific modified hemoglobin-based oxygen-carrying solution, developed for use in veterinary medicine. PolyHbBv was fractionated into four distinct tetrameric and multiple polytetrameric forms ranging in molecular mass (87.2-502.3 kDa) using size exclusion chromatography (SEC) and verified by laser light scattering. We evaluated the structural modification occurring in the fractionated mixture of PolyHbBv and assessed the functionality and redox stability of each fraction in relation to the mixture as a whole. Intramolecular cross-linking evaluation as performed by MALDI-MS and SEC under dissociating conditions revealed no-site-specific tetramer stabilization within the fractions; Intermolecular cross-linking was highly correlated with lysine and histidine modification as determined by amino acid composition analysis. While native unmodified hemoglobin, HbBv, PolyHbBv, and PolyHbBv fractions (F1-F4) revealed significant methionine oxidation, modification, or both, the critical betaMet55 located in the functionally plastic domains (alpha1-beta1 interface) of HbBv was unaltered. Moreover, neither of the two betaCys93 located in the highly plastic alpha1-beta2 interface were modified in PolyHbBv or in F1-F4. Our structural analysis also revealed that the reported loss in sensitivity to chloride in PolyHbBv could not be attributed to direct alteration of chloride ion binding amino acids. Structural modification imparted by glutaraldehyde resulted in nearly identical functional characteristics of PolyHbBv and its fractions with regard to oxygen equilibrium, ligand binding, and autoxidative kinetics.     

A molecular spectroscopic description of optical spectra of J-aggregated dyes on gold nanoparticles

The extinction spectra of J-aggregated dyes on gold nanoparticles, which exhibit interferences between the plasmonic and dye resonances, are simulated by a quantum mechanical model that considers the dye transition to interact through transition-dipole coupling with a continuum of nanoparticle states. This alternative to the classical core-shell dielectric model provides the wavefunctions of the coupled molecule-nanoparticle system and qualitatively explains the enhancement of resonance Raman, fluorescence, and other light-driven processes of molecules adsorbed to nanoparticles.