A theoretical study of calcium microdomains in turtle hair cells.

Confocal imaging has revealed microdomains of intracellular free Ca2+ in turtle hair cells evoked by depolarizing pulses and has delineated factors affecting the growth and dissipation of such domains. However, imaging experiments have limited spatial and temporal resolution. To extend the range of the results we have developed a three-dimensional model of Ca2+ diffusion in a cylindrical hair cell, allowing part of the Ca2+ influx to occur over a small circular region (radius 0.125-1.0 micron) representing a high-density array of voltage-dependent channels. The model incorporated experimental information about the number of channels, the fixed and mobile Ca2+ buffers, and the Ca2+ extrusion mechanism. A feature of the calculations was the use of a variable grid size depending on the proximity to the Ca2+ channel cluster. The results agreed qualitatively with experimental data on the localization of the Ca2+ transients, although the experimental responses were smaller and slower, which is most likely due to temporal and spatial averaging in the imaging. The model made predictions about 1) the optimal Ca2+ channel number and density within a cluster, 2) the conditions to ensure independence of neighboring clusters, and 3) the influence of the Ca2+ buffers on the kinetics and localization of the microdomains. We suggest that an increase in the mobile Ca2+ buffer concentration in high-frequency hair cells (which possess a larger number of release sites) would allow lower amplitude and faster Ca2+ responses and promote functional independence of the sites.     

A theoretical study of acriflavin-DNA binding

A theoretical study of binding behaviour of acriflavin, a well-known mutagen, with DNA base pairs such as AT, GC, TA and CG has been performed using CNDO/2 method to compute net atomic charges and dipoles located at various centres in acriflavine as well as base pairs. Acriflavine-DNA base pair interactions have been evaluated using second order perturbation method with multicentered multipole approximation. Only minimum energy configurations have been reported. Results have been discussed with a view to obtain a comparative behaviour of other similar dyes like proflavine and acridine orange.     

A theoretical study of glucosamine synthase

Continuing our theoretical studies of glucosamine synthase catalysis, we have carried out MNDO and ab initio calculations of the first stage of the reaction, which involves the attack of a cysteine thiol group from the enzyme active site on the side chain carboxyamide group of glutamine, producing ammonia and thioester. The reactants were modelled by methyl mercaptate and acetamide, respectively. For two considered mechanisms of the reaction the energy surfaces were evaluated. Mechanism I, proposed by Chmara et al. (1985) involves the nucleophilic attack of a deprotonated thiol group on the carbonyl carbon atom. Mechanism II, postulated in our previous work (Tempczyk et al. 1989), assumes the concerted binding of the mercaptate sulphur to the carbonyl carbon and the sulfhydryl hydrogen to the amide nitrogen with simultaneous breaking of the S-H bond. The energy surface of mechanism I shows no minimum on the approach of the mercaptide anion towards the carbonyl carbon, which is also consistent with ab initio calculations in a 4-31 G basis set. Therefore, mechanism I seems to be unlikely. The same analysis of mechanism II shows that it leads to the desired products: methyl thioacetate and ammonia. The presence of a sulfhydryl hydrogen causes apparent pyramidicity of the amido nitrogen and lengthening of the C-N bond in the transition state, making conditions for the release of the ammonia molecule. The MNDO calculated energy barrier of the reaction is 50.1 kcal/mol and the approximate 4-31 G ab initio barrier (at the MNDO geometries of the substrate complex and the transition state) is 63 kcal/mol. The biggest energy contribution to the barrier comes from the breaking of the S-H bond, which also causes a large charge separation in the transition state. The latter affect may result in the stabilisation of the transition state in a real enzymatic environment when compared to the gas phase, e.g. by the interaction of the reacting center with a pair of oppositely charged amino acid side chains such as lysinium and glutamate (aspartate), which are present in the enzyme studied. To estimate the magnitude of this effect, molecular mechanics calculations were carried out on the reaction center at the transition state in our proposed model of the enzymatic active site. The site was supplemented by ammonium and acetate ion, which were to mimic the lysinium and glutamate/aspartate side chains. A transition state stabilization energy of 20 kcal/mol was obtained and this lowers the energy barrier to about 30 kcal/mol. This value is within the thermal energy range of an average protein and indicates that our mechanism is a possible route of glucosamine synthase catalysis. Offprint requests to: E. Borowski     

A theoretical study of glucosamine synthase

Glucosamine synthase transfers the -amino group of glutamine to fructose, producing 1-glucosamine which is the key constituent of bacterial and fungal cell walls. In this study, model calculations were performed on substrate binding to the enzyme active site. Two models of the active site of glucosamine synthase were proposed, which assume two different sequences of aminoacids, Cys-Gly-Ile and Cys-Ala-Cys, the first one being the N-terminal sequence of the Escherichia coli enzyme. Several initial geometries were assumed for these tripeptides, the energy was then optimized by means of molecular mechanics. It has been found that the structure which is both energy optimal and satisfies the assumed cysteine sulphur arrangement consists of combinations of C ₇ ^eq and C ₇ ^ax conformations of single residues. Molecular mechanics calculations were then performed on glutamine and d-fructose-6-phosphate, which are the substrates of the enzymatic satalysis, and on their complex with the enzyme glutamine-binding site. The spatial configuration of the compounds under study, which is optimal as far as the reaction path is concerned, also turned out to be an energy minimum.     

Building the mammalian heart from two sources of myocardial cells

Cardiogenesis is an exquisitely sensitive process. Any perturbation in the cells that contribute to the building of the heart leads to cardiac malformations, which frequently result in the death of the embryo. Previously, the myocardium was thought to be derived from a single source of cells. However, the recent identification of a second source of myocardial cells that make an important contribution to the cardiac chambers has modified the classical view of heart formation. It also has an important influence on the interpretation of mutant phenotypes in the mouse, with consequences for the classification and prognosis of human congenital heart defects.     

The coating of mouse myocardial cells. A cytochemical electron microscopical study.

The coating of mouse myocardial cells has been investigated with a variety of cytochemical methods. The coating of the surface membrane gives a positive reaction with ruthenium red, colloidal thorium, phosphotungstic acid (PTA) at low pH, silver methenamine after periodic oxidation (PA-silver technique) and with silver proteinate after periodic oxidation and thiocarbohydrazide treatment (PA-TCH-silver technique). The coating of the T system gives almost similar results. The nexuses do not react with PTA nor with the PA-silver and PA-TCH-silver techniques, but they are strongly stained with ruthenium red which reveals periodic structures in their gaps. The specificities of the colloidal thorium technique and PAT staining have been tested by chemical treatments (methylation, acetylation, saponification), enzymatic digestions (pronase, trypsin, hyaluronidase, neuraminidase) and carbohydrate extractions (with 0.1 N NaOH and 0.05 M H2SO4). These cytochemical data indicate, considering the specificity of the reactions, that the coating of the membrane surface and the T system contains polyanionic groups. A part of them, at least, would belong to a carbohydrate-containing material (glycoproteins), whereas at the level of nexuses the sugar residues would probably be absent.     

A theoretical study of the attenuation control mechanism

The attenuator control mechanism, used in a number of amino acid biosynthetic operons, is considered from a theoretical point of view. The physics of RNA hairpin-loop formation is discussed, and rules for predicting which codons in the leader peptide that will affect operon expression are suggested. Manabe's (1981) stochastic model for the attenuator mechanism is used to analyse a number of known attenuators, showing a need for a “polymerase pause-site” in most of the attenuators, and providing some quantitative arguments in favour of the use of unusual codons in the control region.     

A theoretical study of polymorphism in VQIVYK fibrils

The VQIVYK fragment from the Tau protein, also known as PHF6, is essential for aggregation of Tau into neurofibrillary lesions associated with neurodegenerative diseases. VQIVYK itself forms amyloid fibrils composed of paired β-sheets. Therefore, the full Tau protein and VQIVYK fibrils have been intensively investigated. A central issue in these studies is polymorphism, the ability of a protein to fold into more than one structure. Using all-atom molecular simulations, we generate five stable polymorphs of VQIVYK fibrils, establish their relative free energy with umbrella sampling methods, and identify the side chain interactions that provide stability. The two most stable polymorphs, which have nearly equal free energy, are formed by interdigitation of the mostly hydrophobic VIY “face” sides of the β-sheets. Another stable polymorph is formed by interdigitation of the QVK “back” sides. When we turn to examine structures from cryo-electron microscopy experiments on Tau filaments taken from diseased patients or generated in vitro, we find that the pattern of side chain interactions found in the two most stable face-to-face as well as the back-to-back polymorphs are recapitulated in amyloid structures of the full protein. Thus, our studies suggest that the interactions stabilizing PHF6 fibrils explain the amyloidogenicity of the VQIVYK motif within the full Tau protein and provide justification for the use of VQIVYK fibrils as a test bed for the design of molecules that identify or inhibit amyloid structures.     

A theoretical study of the dielectric constant of protein

The dielectric properties of a protein molecule were investigated by calculating a 'local dielectric constant' with the aid of normal mode analysis. This local dielectric constant was calculated from the electronic polarization of atoms and the orientational polarization of local dipoles. The former was obtained from atomic polarizations of the whole atoms in a protein molecule. The latter was determined from the fluctuation-dissipation theorem. The degree of dipole fluctuation was calculated from the positional fluctuation of each atom obtained by the normal mode analysis. Assuming a minimum volume for a continuum model, the resulting local dielectric constants ranged from 1 to 20 inside the protein.     

A theoretical study of double-inhibitor-titration curves in free-energy-transducing networks

The general relationship between the double-inhibitor-titration curves and the kinetic properties of pumps in a delocalized chemiosmotic free-energy-transducing network is studied. The kinetic conditions for a delocalized system to generate the observed double-inhibitor-titration results are derived and the effectiveness of double-inhibitor experiments in discriminating between the localized and the delocalized proton-coupling mechanisms is assessed. It is found that, using simple enzymatic cycles for the kinetics of the pumps in a delocalized network, one can reproduce the experimentally measured double-inhibitor-titration curves that were widely used to argue against the delocalized mechanism. This implies that double-inhibitor-titration curves alone are not sufficient to discriminate between localized and delocalized coupling systems. Additional information concerning the kinetic responses of isolated pumps on the proton gradient across the membrane and inhibitor concentrations are required.     

The protonation of peptides: A non-empirical theoretical study

The energy surface resulting from the protonation of the peptide unit, OCNH, has been calculated non-empirically using the LCAO MO SCF (Gaussian function) method. Providing that rotation of the NH₂⁺ group is permitted, N-protonation is favoured. However a nearly equal energy minimum was obtained for O-protonation, suggesting that when rotation is not permitted, or when two hydrogens are originally present, O-protonation is favoured.     

A theoretical study of double-inhibitor-titration curves in free-energy-transducing networks

The general relationship between the double-inhibitor-titration curves and the kinetic properties of pumps in a delocalized chemiosmotic free-energy-transducing network is studied. The kinetic conditions for a delocalized system to generate the observed double-inhibitor-titration results are derived and the effectiveness of double-inhibitor experiments in discriminating between the localized and the delocalized proton-coupling mechanisms is assessed. It is found that, using simple enzymatic cycles for the kinetics of the pumps in a delocalized network, one can reproduce the experimentally measured double-inhibitor-titration curves that were widely used to argue against the delocalized mechanism. This implies that double-inhibitor-titration curves alone are not sufficient to discriminate between localized and delocalized coupling systems. Additional information concerning the kinetic responses of isolated pumps on the proton gradient across the membrane and inhibitor concentrations are required.     

A theoretical study of glucose mutarotation in aqueous solution

In this work the mechanism of glucose mutarotation is investigated in aqueous solution considering the most likely pathways proposed from experimental work. Two mechanisms are studied. The first involves an intramolecular proton transfer as proposed by textbooks of organic chemistry, and the second uses one solvent water molecule to assist proton transfer. Both mechanisms are studied in the gas phase and in aqueous solution with the help of a polarizable continuum model, which is adopted to introduce the electrostatic nonspecific influence of bulk solvent. The structures are fully characterized through the calculation of the corresponding vibrational frequencies. The rate coefficients for each mechanism are calculated following transition-state theory in both the gas phase and in aqueous solution. Values computed for the water-assisted pathway in the continuum solvent agree best with the experimental results.     

A theoretical study of lipid-protein interactions in bilayers.

We present a theoretical study of the effect of different types of lipid-protein interactions on the thermodynamic properties of protein-containing lipid bilayers. The basis of this work is a theoretical model for pure lipid bilayer phase transitions developed earlier by Scott. Simple assumptions on the nature of the lipid conformations near a protein strongly affect the predicted properties of the model. Here we consider (a) random protein-lipid contacts, (b) enhanced contact between protein and lipid with a number of gauche bonds, and (c) enhanced contact between protein and all-trans but tilted lipid chains. Comparison of predicted results with experimental data seems to favor point c above but, by itself point c does not work well at larger protein concentrations. The results are discussed in the light of spectroscopic data, lipid-protein (plus annular lipid) miscibility, and interprotein forces.     

A study on the preservation of the beating rhythm of single myocardial cells in vitro

Single myocardial cells from fetal mouse heart beat spontaneously in monolayer culture. In standard medium they maintained constant beating rates for at least 5 h at 37 °C. When the beats of single myocardial cells were stopped for a short time by treatment with EGTA, or slowed down by incubating the cells in medium of low pH, the original beating rates could be restored by replacing the cells in the original medium. The same procedure also restored the rates after they had been disturbed by incubating the cells in medium of low sodium and high potassium ion content. Moreover, the original beating rates could be restored after keeping the cells at 10 °C for 22–24 h, but not after keeping them at 37 °C for 22–24 h.     

Ultrastructure of myocardial widened Z bands and endocardial cells in two teleostean species

Summary Widened myocardial Z bands and endocardial cells are described in two teleostean species Cichlasoma meeki and Corydoras aeneus. Widened Z bands containing mainly amorphous and electron-dense material were seen in a number of myocardial cells. Further, similar material may occur in large amounts beneath the sarcolemma and at intercellular junctions. Occasionally, we observed continuity between the latter material and that in expanded Z bands.In C. meeki the ventricular endocardial layer consists of two structurally different cell types, whereas in C. aeneus only one cell type was seen. The functional aspects of widened Z bands are discussed.