Mathematical modeling of the myosin light chain kinase activation

The mathematical model presented here describes the interactions among Ca2+, calmodulin (CaM), and myosin light chain kinase (MLCK) and consists of a kinetic scheme taking into account 7 reactions instead of 12 as proposed previously. We derive a system of 5 nonlinear ordinary differential equations. Solving it yields the prediction of active MLCK as a function of [Ca2+] whereby the active MLCK is defined to be proportional to the Ca4CaM.MLCK complex concentration. The model predictions are compared with other theoretical and experimental predictions of active MLCK as well as with the results of our previously proposed complex model.     

Electrospray ionization mass spectrometry studies of noncovalent myosin VI complexes reveal a new specific calmodulin binding site

Among the myosin superfamily, myosin VI differs from all others by a reverse directionality and a particular motility. Little structural information is available for myosin VI. It is known that it binds one calmodulin (CaM) by means of a single "IQ motif" and that myosin VI contains a specific insert located at the junction between the motor domain (MD) and the lever arm, likely to play a critical role for the unusual motility previously observed. Electrospray ionization mass spectrometry (MS) was used to determine the CaM and Ca2+ stoichiometries in several myosin VI constructs. In particular, the experimental conditions required for the observation of multiprotein/Ca2+ noncovalent assemblies are detailed for two truncated MD constructs (less than 20 kDa) and for three full MD constructs (more than 90 KDa). The specificity of the detected stoichiometries is discussed for each construct and the resolving power of Time of Flight mass spectrometry is stressed, in particular for the detection of metal ions binding to high molecular weight complexes. MS reveals a new CaM binding site for myosin VI and highlights a different behavior for the five myosin VI constructs versus Ca2+ binding. In addition to these stoichiometry based experiments, gas-phase dissociation analyses on intact complexes are described. They reveal that Ca2+ transfer between protein partners occurs during the dissociation process for one construct with a full MD. Charge-transfer and dissociation behavior has allowed to draw structural assumptions for the interaction of the MD with the CaM N-terminal lobe.     

A formal [3 + 3] cycloaddition reaction. 5. An enantioselective intramolecular formal aza-[3 + 3] cycloaddition reaction promoted by chiral amine salts

A detailed account on chiral secondary amine salt promoted enantioselective intramolecular formal aza-[3 + 3] cycloadditions is described here for the first time. The dependence of enantioselectivity on the structural feature of these chiral amines is thoroughly investigated. This study also reveals a very interesting reversal of the stereochemistry in the respective cycloadducts obtained using C(1)- and C(2)-symmetric amine salts. In addition, the influence of solvents, counteranions, and temperatures on the enantioselectivity is described, and a unified mechanistic model based on experimental results as well as semiempirical calculations is proposed.     

Parameterization of Ca+2-protein interactions for molecular dynamics simulations

Molecular dynamics simulations of Ca+2 ions near protein were performed with three force fields: GROMOS96, OPLS-AA, and CHARMM22. The simulations reveal major, force-field dependent, inconsistencies in the interaction between the Ca+2 ions with the protein. The variations are attributed to the nonbonded parameterizations of the Ca+2-carboxylates interactions. The simulations results were compared to experimental data, using the Ca+2-HCOO- equilibrium as a model. The OPLS-AA force field grossly overestimates the binding affinity of the Ca+2 ions to the carboxylate whereas the GROMOS96 and CHARMM22 force fields underestimate the stability of the complex. Optimization of the Lennard-Jones parameters for the Ca+2-carboxylate interactions were carried out, yielding new parameters which reproduce experimental data.     

Implication of phosphorylation of the myosin II regulatory light chain in insulin-stimulated GLUT4 translocation in 3T3-F442A adipocytes

In adipocytes, insulin stimulates glucose transport primarily by promoting the translocation of GLUT4 to the plasma membrane. Requirements for Ca(2+)/calmodulin during insulin-stimulated GLUT4 translocation have been demonstrated; however, the mechanism of action of Ca(2+) in this process is unknown. Recently, myosin II, whose function in non-muscle cells is primarily regulated by phosphorylation of its regulatory light chain by the Ca(2+)/calmodulin-dependent myosin light chain kinase (MLCK), was implicated in insulin-stimulated GLUT4 translocation. The present studies in 3T3-F442A adipocytes demonstrate the novel finding that insulin significantly increases phosphorylation of the myosin II RLC in a Ca(2+)-dependent manner. In addition, ML-7, a selective inhibitor of MLCK, as well as inhibitors of myosin II, such as blebbistatin and 2,3-butanedione monoxime, block insulin-stimulated GLUT4 translocation and subsequent glucose transport. Our studies suggest that MLCK may be a regulatory target of Ca(2+)/calmodulin and may play an important role in insulin-stimulated glucose transport in adipocytes.     

The dependence of reduced plate height on reduced velocity in carbon dioxide supercritical fluid chromatography with packed columns

Summary The relation is proposed for the dependence of reduced plate height, h, on reduced velocity in carbon dioxide, supercritical fluid chromatography with packed columns. The classical Knox model does not take into account the density drop in the column which produces a peak-broadening. A supplementary coefficient with a parabolic dependence on velocity must be added and then a good fit between experimental results and theory is observed. Finally, the influence of other parameters such as pressure, capacity factor and solute molecular area is discussed.     

Ultrafine Na-4-mica: uptake of alkali and alkaline earth metal cations by ion exchange

The cation exchange properties of alkali and alkaline earth metal cations at room temperature were investigated on an ultrafine, highly charged Na-4-mica (with the ideal mica composition Na4Mg6Al4Si4O20F4.xH2O). Ultrafine mica crystallites of 200 nm in size led to faster Sr2+ uptake kinetics in comparison to larger mica crystallites. The alkali metal ion (K+, Cs+, and Li+) exchange uptake was rapid, and complete exchange occurred within 30 min. For the alkaline earth metal ions Ba2+, Ca2+, and Mg2+, however, the exchange uptake required lengthy periods from 3 days to 4 weeks to be completed, similar to its Sr uptake, as previously reported. Kinetic models of the modified Freundlich and parabolic diffusion were examined for the experimental data on the Ba2+, Ca2+, and Mg2+ uptakes. The modified Freundlich model described well the Ba2+ ion uptake kinetics as well as that for the Sr2+ ion, while for the Ca2+ and Mg2+ ions the parabolic diffusion model showed better fitting. The alkali and alkaline earth ion exchange isotherms were also determined in comparison to the Sr2+ exchange isotherm. The thermodynamic equilibria for these cations were compared by using Kielland plots evaluated from the isotherms.     

LIQUID-PHASE ADSORPTION KINETICS OF ISOMALTOTRIOSE ON Ca^2＋ EXCHANGE RESIN

The adsorption of isomaltotriose from aqueous solution on Ca2+ resin was investigated.The adsorption isotherm and the rate curve were determined. The pseudo-first-order model,pseudo-second-order model and the intraparticle diffusion model were used to predict the rate constants of adsorption. The activation energy of adsorption has been also evaluated using the pseudo-second-order rate constants. The results showed that the adsorption of isomaltotriose onto Ca2+ resin is an exothermically activated process. The adsorption isotherm can be described by Langmuir equation. The pseudo-second-order model can fit well to the adsorption rate curve of isomaltotriose onto Ca2+ resin. It suggests that the adsorption of isomoltotriose onto Ca2+ resin involve chemical adsorption.     

LIQUID-PHASE ADSORPTION KINETICS OF ISOMALTOTRIOSE ON Ca~(2+) EXCHANGE RESIN

1. INTRODUCTION Oligosaccharide is a carbohydrate comprising 2~9 monosaccharide units linked together by glucoside bond. In the digestive system of humankind, there exits no enzyme for the hydrolysis of oligosaccharides. So it can be used by bifidobacteria in large intestine, and lead to some special physiological function [1]. Oligosaccharide exits in many plants, for example, Morinda officinalis, a precious herb growing in south China. In this herb, four oligosaccharides with the funct…     

Breakthrough characteristics of volatile organic compounds in the -10 to + 170 degrees C temperature range on Tenax TA determined by microtrap technology

In this work the breakthrough volumes (BTVs) of volatile organic compounds (VOCs) on Tenax TA were determined in the -10 to 170 degrees C temperature range by using microtrap (MT) technology. The MT technology allowed experimental investigation of the temperature dependence of BTVs. Along with the BTV data, we also discuss the thermodynamics of the temperature dependence of the BTV through a two-parameter equation In (BTV) = A1/T + C1 where T is temperature (K), A1 = -deltaH/R where deltaH is enthalpy of sorption and C1 is constant. This equation fitted well the experimental results with R2 values between 0.9737 (acetone) and 0.9995 (dimethyl disulfide), with n between 6 and 11. However, for n-pentane, n-hexane and 1-hexene it proved that a three parameter equation In (BTV) = A2/ T + BTB + C2 fitted better to the experimental results, with A2 = -deltaHT0/R, B = deltaCp/R, TB = 1n(T/T0) + (T0 - T)/T, C2 a constant, deltaHT0 the adsorption enthalpy at reference temperature T0 and deltaCp the difference in the molar heat capacity of compound under investigation between the sorbed and the free gas phase state. The statistical analysis showed for example for n-pentane now R2 = 0.9969 instead of R2 = 0.9746, and Fisher statistics F = 487 instead of F = 153, with a significance level P = 0.018 for the third parameter. The results show that microtrap technology well serves as a technology to get information on temperature dependence of BTVs in an extended range. Simultaneously, it turns out that MT technology, extending the operational temperature range, is well served by a careful investigation of the temperature dependence models of BTVs.     

Docking of ATP to Ca-ATPase: considering protein domain motions

Most standard molecular docking algorithms take into account only ligand flexibility, while numerous studies demonstrate that receptor flexibility may be also important. While some efficient methods have been proposed to take into account local flexibility of protein side chains, the influence of large-scale domain motions on the docking results still represents a challenge for computational methods. In this work we compared the results of ATP docking to different models of Ca-ATPase: crystallographic apo- and holo-forms of the enzyme as well as "flexible" target models generated via molecular dynamics (MD) simulations in water. MD simulations were performed for two different apo-forms and one holo-form of Ca2+-ATPase and reveal large-scale domain motions of type "closure", which is consistent with experimental structures. Docking to a set of MD-conformers yielded correct solutions with ATP bound in both domains regardless of the starting Ca2+-ATPase structure. Also, special attention was paid to proper ranking of docking solutions and some particular features of different scoring functions and their applicability for the model of "flexible" receptor. Particularly, the results of docking ATP were ranked by a scoring criterion specially designed to estimate ATP-protein interactions. This criterion includes stacking and hydrophobic interactions characteristic of ATP-protein complexes. The performance of this ligand-specific scoring function was considerably better than that of a standard scoring function used in the docking algorithm.     

An ignored but most favorable channel for NCO+C2H2 reaction

The NCO+C(2)H(2) reaction has been considered as a prototype for understanding the chemical reactivity of the isocyanate radical towards unsaturated hydrocarbons in fuel-rich combustion. It has also been proposed to provide an effective route for formation of oxazole-containing compounds in organic synthesis, and might have potential applications in interstellar processes. Unfortunately, this reaction has met mechanistic controversy both between experiments and between experiments and theoretical calculations. In this paper, detailed theoretical investigations at the Becke's three parameter Lee-Yang-Parr-B3LYP6-31G(d), B3LYP6-311++G(d,p), quadratic configuration interaction with single and double excitations QCISD6-31G(d), and Gaussian-3 levels are performed for the NCO+C(2)H(2) reaction, covering various entrance, isomerization, and decomposition channels. Also, the highly cost-expensive coupled-cluster theory including single and double excitations and perturbative inclusion of triple excitations CCSD(T)/aug-cc-pVTZ single-point energy calculation is performed for the geometries obtained at the Becke's three parameter Lee-Yang-Parr-B3LYP6-311++G(d,p) level. A previously ignored yet most favorable channel via a four-membered ring intermediate with allyl radical character is found. However, formation of P(3) H+HCCNCO and the five-membered ring channel predicted by previous experimental and theoretical studies is kinetically much less competitive. With the new channel, master equation rate constant calculations over a wide range of temperatures (298-1500 K) and pressures (10-560 Torr) show that the predicted total rate constants exhibit a positive-temperature dependence and no distinct pressure dependence effect. This is in qualitative agreement with available experimental results. Under the experimental conditions, the predicted values are about 50% lower than the latest experimental results. Also, the branching ratio variations of the fragments P(2) HCN+HCCO and P(5) OCCHCN+H as well as the intermediates L1 HCHCNCO, r4 cCHCHNC-O, and L5 NCHCHCO are discussed with respect to the temperature and pressure. Future experimental reinvestigations are strongly desired to test the newly predicted channel for the model NCO+C(2)H(2) reaction. Implications of the present results in various fields are discussed.     

A quantitative model of preferential evaporation and retention for atom probe tomography

It is well known that the apparent concentration of a solute element in metal, detected by atom probe tomography analysis, depends on the measurement condition such as specimen temperature, pulse fraction, and pulse frequency. The dependence was qualitatively interpreted to be caused by preferential evaporation and retention in field evaporation. A quantitative physical model accounting for the preferential evaporation and retention was proposed herein for the first time. The proposed model was applied to a ferritic iron–copper (Fe–Cu) alloy for preferential evaporation and a ferritic iron–silicon (Fe–Si) alloy for preferential retention. The model explained the temperature dependence on the apparent concentration of the solute element and the unwindowed background noise in each alloy well, whereas the dependence of pulse fraction and pulse frequency was not completely explained. The cause of the difference between the experimental and calculated results based on the model was discussed. Copyright © 2014 John Wiley & Sons, Ltd.     

Oxidation of toluidine blue by chlorite in acid and mechanisms of the uncatalyzed and Ru(III)-catalyzed reactions: a kinetic approach

The complex mechanism of the uncatalyzed and Ru(III)-catalyzed oxidation of toluidine blue [(7-amino-8-methylphenothiazin-3-ylidene)dimethyl ammonium chloride, TB(+)Cl(-)] (λ(max) = 626 nm) by acidic chlorite is elucidated by a kinetic approach. Both the uncatalyzed and catalyzed reactions had a first-order dependence on the initial ClO(2)(-) and H(+) concentrations ([ClO(2)(-)](0) and [H(+)](0), respectively). The catalyzed reaction had a first-order dependence on the initial Ru(III) concentration ([Ru(III)](0)). The overall reaction of toluidine blue and chlorite ion was as follows: TB(+) + 5ClO(2)(-) + H(+) = P + 2ClO(2) + 2HCOOH + 3Cl(-) + H(2)O, where P is (7-amino-8-methyl-5-sulfoxophenothiazin-3-ylidene)amine. Consistent with the experimental results, the pertinent reaction mechanisms are proposed.     

Elemental analysis within the electrical double layer using total reflection X-ray fluorescence technique

A simplified total reflection X-ray fluorescence (TRXF) technique is proposed for the study of the electrical double layer (EDL) near charged monolayers at the air-water interface. In contrast to the parent NTEF (near total external reflection X-ray fluorescence) method, TRXF uses a fixed angle of incidence (below the critical one) and abandons both "spatial resolution" (which is poor anyway) and "absolute calibration" with the bulk reference. These modifications reduce both the duration of experiments and the complexity of the data treatment by 1-2 orders of magnitude and turn TRXF into a truly simple tool for elemental analysis within the EDL. A few TRXF experiments appear sufficient to disprove the model of simultaneous binding of alkali earth metal cations and inorganic anions to negatively charged phospholipid monolayers as proposed in literature. Direct experimental support was provided to the essential feature of the EDL near highly charged interfaces: The main amount of counterions is concentrated in the thin inner part of the EDL irrespective of the electrolyte concentration in the bulk. A study of the counterion competition for the participation in the EDL of highly negatively charged behenylsulfate (BS) monolayers (resulting from packing density limitations) revealed that univalent Cs+ is quite competitive with divalent Ca2+ and Ba2+ (which contradicts the classical Gouy-Chapman model). If the univalent/divalent ion ratio in bulk is 9:1, the corresponding ratio in the EDL is ca. 1.5 for Cs+/Ca2+ and 0.5 for Cs+/Ba2+, whereas the model predicts 0.14 only. Bearing in mind packing density limitations, these values are consistent with a series of sizes for hydrated ions: Cs+ < Ba2+ < Ca2+.     

Erythrocyte troponin inhibitor-like protein: isolation and characterization.

A protein was isolated from a human erythrocyte lysate with an apparent molecular weight of 23,000--24,000 daltons. This protein was purified by batch DEAE cellulose followed by column DEAE cellulose chromatography and a gradient of NaCl. On sodium dodecyl sulfate acrylamide electrophoresis, the erythrocyte protein comigrated with muscle troponin inhibitor. An isoelectric precipitation (pH 9.25) was used for the separation of muscle troponin inhibitor from a complex with another troponin component. Both the erythrocyte protein and the muscle troponin inhibitor partially inhibited muscle myosin Ca2+ and K+-EDTA ATPase activity. Furthermore, they inhibited actin-activated Mg2+-ATPase of muscle myosin. The inhibitory effects were absent in the presence of muscle troponin calcium-binding component. Muscle troponin inhibitor and the erythrocyte troponin inhibitor-like protein bound to muscle myosin when myosin was precipitated twice at low ionic strength. The presence of a troponin inhibitor-like protein in erythrocytes suggests that it may be a component in the regulation of contractile activity.     

Surface properties of various powdered hydroxyapatites

Electrophoretic mobilities of various synthetic and semisynthetic hydroxyapatites (Ca10(PO4)6(OH)2, HAP) suspended in aqueous solutions have been measured as a function of pH and calcium concentration. The studied powders differ in particle size, crystallinity degree and surface contamination (carbonate). When equilibrated in mineral acids or bases, a large plateau of negative mobility is observed in the pH range 5-8, with increasing negative values at higher pH. Only in the case of the sample composed of nanoparticles, positive mobility obtains at pH < 8.9. When Ca2+ is added, positive mobility values are observed for all samples, and a bell-shaped profile results as a function of pH. Two possible models are explored to describe the results: the Nernstian approach, which assumes solubility equilibrium and surface potentials determined by the three potential-determining ions (Ca2+, PO3-4, and OH-), and the surface complexation approach, based on the idea of negligible phase transfer of structural phosphate. The Nernstian model is inadequate, whereas a very simple surface complexation model based on the equations Ca5(PO4)+3 = Ca4(PO4)-3 + Ca2+,Ca4(PO4)-3 + H+ = Ca4(PO4)2(PO4H),Ca5(PO4)+3 + OH- = Ca5(PO4)3(OH),coupled with a very simple electrical double layer, model suffices to reproduce the bell-shaped profile of the mobility as a function of pH in the presence of added calcium salts. The results also show that the sample composed of nanoparticles exchanges ions more easily with the solution, without reaching the solubility equilibrium in the explored timespans. In the presence of soluble phosphate salts, it is postulated that the same surface ensembles define the surface charge, with participation of phosphate as described by the equation Ca5(PO4)+3 + PO3-4 = Ca4(PO4)-3.HAP is just one member of a family of calcium phosphates with different (Ca)/(P) ratios. Electrophoretic mobilities of another member, tricalcium diphosphate, Ca3(PO4)2, were also measured and shown to be described by the same basic model. Comparison with previous literature data shows that the negative plateau in the mobility is a general feature of many HAP samples at low Ca2+, again in agreement with the surface complexation model. FTIR data demonstrates that surface phosphate indeed undergoes protonation, as postulated in the model.     

Structural transitions as determinants of the action of the calcium-dependent antibiotic daptomycin

Daptomycin is a cyclic anionic lipopeptide antibiotic recently approved for the treatment of complicated skin infections (Cubicin). Its function is dependent on calcium (as Ca2+). Circular dichroism spectroscopy indicated that daptomycin experienced two structural transitions: a transition upon interaction of daptomycin with Ca2+, and a further transition upon interaction with Ca2+ and the bacterial acidic phospholipid, phosphatidyl glycerol. The Ca2+-dependent insertion of daptomycin into model membranes promoted mild and more pronounced perturbations as assessed by the increase of lipid flip-flop and membrane leakage, respectively. The NMR structure of daptomycin indicated that Ca2+ induced a conformational change in daptomycin that increased its amphipathicity. These results are consistent with the hypothesis that the association of Ca2+ with daptomycin permits it to interact with bacterial membranes with effects that are similar to those of the cationic antimicrobial peptides.     

A thermodynamic surface model for caesium sorption on bentonite

Caesium sorption on Wyoming bentonite MX-80 has been studied in solutions of NaCl, KCl, MgCl(2), CaCl(2), NaNO(3) and Ca (NO(3))(2) of concentrations varying between 0.025 and 1 mol/L, as well as in a weakly saline (I=0.004 ml/L) and a strongly saline (I=0.46 mol/L) natural groundwater. These experiments have been used to derive a thermodynamic model for the interaction of caesium with the bentonite surface in accordance with a surface chemical model, including acid/base reactions developed recently for montmorillonite. The sorption behaviour of caesium on bentonite can be described, within the experimental and model uncertainties, in terms of a one-site ion exchange model. The ion exchange constant obtained for the reaction NaX+Cs(+) left arrow over right arrow CsX+Na(+) (where X represents the ion exchange sites on montmorillonite) is log(10) K(0)(ex)=1.6. Impurities in the bentonite, influencing the concentrations of competing cations, such as Na(+), K(+), Mg(2+) and Ca(2+), have a crucial impact on the sorption of caesium. This impact can be adequately quantified with the present model. The model predictions compare well with sorption data published in the open literature on both Wyoming bentonite MX-80 and other types of bentonite. Distribution coefficients from the literature obtained from both batch and diffusion experiments and varying over four orders of magnitude are reproduced and explained successfully by the model.     

Complexation of polyacrylates by Ca2+ ions. Time-resolved studies using attenuated total reflectance Fourier transform infrared dialysis spectroscopy

The attenuated total reflectance Fourier transform infrared dialysis technique is introduced for the time-resolved investigation of the binding processes of Ca2+ to polyacrylates dissolved in water. We observed transient formation of intermediates in water with various types of coordination of the carboxylate group to Ca2+ throughout the complexation steps. Time-resolved changes in the spectra were analyzed with principal component analysis, from which the spectral species were obtained as well as their formation kinetics. We propose a model for the mechanisms of Ca2+ coordination to polyacrylates. The polymer chain length plays an important role in Ca2+ binding.