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PubMed1985

Localization of the parallel elastic components in frog skinned muscle fibers studied by the dissociation of the A- and I-bands.

Localization of the parallel elastic components (PECs) in skinned muscle fibers was investigated by analyzing the change of the resting tension, which accompanies the dissociation of the A- and I-bands. The A-band was dissociated from both ends by increasing the concentration of KCl under relaxing conditions (0.09-0.54 M KCl, 4.0 mM MgATP, 1.0 mM Mg2+, 4.0 mM EGTA, pH 6.0-9.0, 20 degrees C). At sarcomere lengths greater than or equal to 3.5 microns, the length of the A-band was estimated by comparing the intensity of the first-order optical diffraction line with the results of model calculations. These results were supported by differential-interference microscopy and sodium dodecyl sulfate gel electrophoresis. It was shown that the resting tension decreased nearly in proportion to the residual length of the A-band. At sarcomere lengths less than or equal to 4.0 microns, the resting tension after the dissociation of the A-band was lowered to less than 10% of the initial value. On the other hand, at sarcomere lengths greater than or equal to 5.0 microns the resting tension after the dissociation of the A-band still showed approximately 35% of the initial value and did not change even after the I-band was dissociated by a solution containing KI. From these results, we propose that most of the PECs contributing to resting tension bind almost uniformly to the A-band and there are also PECs connecting Z-lines.

Actins↗
PubMed1993

Acid-induced dissociation of alpha A- and alpha B-crystallin homopolymers.

Homopolymers were constructed from the alpha A and alpha B polypeptides isolated from the lens protein alpha-crystallin. As the pH is lowered from 7.0 to 3.4, these homopolymers dissociate to smaller species with molecular masses ranging from 80 to 250 kDa for the alpha A and around 140 kDa for the alpha B dissociation products. The pKa for this dissociation was 3.8 +/- 0.2 for alpha A and 4.1 +/- 0.1 for alpha B homopolymers. Further decreases in pH, to 2.5, resulted in the presence of only denatured alpha B polypeptides, whereas the alpha A dissociation products remained intact. Fractionation of the acid dissociation products from the alpha A homopolymer at pH 2.5 yielded stable species with molecular masses of 220 +/- 30, 160 +/- 20, and 90 +/- 10 kDa. The majority of the population at acid pH consisted of the 160 kDa species. Conformational analysis of these species revealed that most of the secondary structure of the original alpha A homopolymer was retained but that the tertiary structure was perturbed. Fluorescence quenching and energy transfer measurements suggested that the molecule had undergone acid expansion, with the greatest perturbation observed in the smallest particles. The results from this work suggest that alpha A homopolymers are heterogeneous populations of aggregates of a "monomeric" molecule with a molecular mass of 160 kDa. This "monomeric" molecule may be formed from the association of two tetrameric units.

Amino Acids↗
PubMed2002

Calcium current components in intact and dissociated adult mouse sympathetic neurons.

We examined which types of high threshold Ca(2+) channels are activated by depolarization in intact and dissociated sympathetic neurons from adult mouse superior cervical ganglia (SCG). Ba(2+) currents were recorded with microelectrodes and discontinuous voltage clamp from neurons in intact ganglia, and using the perforated patch clamp technique in dissociated cells. Peak current was larger in intact neurons, although the voltage dependence was similar. Successive application of omega-conotoxin GVIA, omega-conotoxin MVIIC and nifedipine revealed that the total current in intact cells was composed by 29% N-type, 13% P/Q-type, 32% L-type and 26% resistant to blockade (R-type). In dissociated cells, the N component was larger and the L component smaller, whereas P/Q-type and R-type were similar. Peak currents evoked with an action potential waveform instead of a square pulse were larger in both preparations but the proportions of each component were similar. We conclude that dissociating and culturing somata results in data that only partially reflect the situation in intact neurons. Assuming that the main effect of dissociation is the removal of mature dendritic membrane, the data suggest that L channels are more abundant on dendrites and N channels on the soma of intact sympathetic neurons, whereas P/Q and R channels may be uniformly distributed over the cell surface. Finally, in intact SCG neurons from rats, the proportions of current evoked by a pulse were: 49% N-type, 11% P/Q-type, 21% L-type and 20% R-type when nifedipine was applied last, suggesting that there are species differences in the expression of L and N channels.

Action Potentials↗
PubMed2003

Dissociation of E-4031 from the HERG channel caused by mutations of an amino acid results in greater block at high stimulation frequency.

OBJECTIVE: We have reported identification of the amino acid whose mutation reduces effects of quinidine on the HERG channel. Although the residue (isoleucine at 647) is not in the recently reported methanesulfonanilide binding site, a single concentration of E-4031 (10 microM) was less effective to I647 mutant channels than wild type HERG channel. We designed the present experiment to further investigate influence of mutations at 647 on the effects of methanesulfonanilides. METHODS AND RESULTS: HERG channels were expressed in Xenopus oocytes and their currents were measured by a two-microelectrode voltage clamp method. Of the two mutations initially studied (I647A and I647F), the I647F had a greater influence and differentially affected the effects of dofetilide and E-4031. The IC(50) for dofetilide of the two mutant channels (I647A and I647F) was increased only 2-fold, but the IC(50) for E-4031 was increased 6-fold (I647A) and 14-fold (I647F). Aromatic residues other than phenylalanine were then substituted for I647, and found to reduce the effects of E-4031. Whereas E-4031 dissociated from the mutant channels during rested state, dofetilide little dissociated. The mutant channels that showed recovery from E-4031 block were inhibited greater at 1 Hz than at 0.1 Hz. CONCLUSIONS: The present results indicate that dissociation of a drug from the HERG channel results in greater block at high frequency. Although the mechanism by which the mutations cause the dissociation of E-4031 is uncertain, it is noteworthy that one methanesulfonanilide dissociates from the channel more easily than another.

Animals↗
PubMed1997

General equation for calculating the dissociation constants of polyprotic acids and bases from measured retention factors in high-performance liquid chromatography.

A general equation relating the observed retention factor to the pH of the mobile phase, the dissociation constants, and the retention factors of the different ionic species has been derived. This equation is applicable to polyprotic weak acid and base dissociation events, that is, the secondary equilibria existing in the HPLC mobile phase. It is written as: [formula: see text] where the kr values are the retention factors of the dissociated species, and Ka(r), the product of the first r-dissociation constants, [formula: see text] is related to the pH of the mobile phase: x = 2.303.pH. The derived equation was used to calculate three dissociation constants of leukotriene E4. Also, a formula is established for calculating the range of pH values where an ionic species is most likely to be predominant in the mobile phase.

Acids↗
PubMed2003

A fractal analysis of analyte-estrogen receptor binding and dissociation kinetics using biosensors: environmental effects.

A fractal analysis is used to model the binding and dissociation kinetics between analytes in solution and estrogen receptors (ER) immobilized on a sensor chip of a surface plasmon resonance (SPR) biosensor. Both cases are analyzed: unliganded as well as liganded. The influence of different ligands is also analyzed. A better understanding of the kinetics provides physical insights into the interactions and suggests means by which appropriate interactions (to promote correct signaling) and inappropriate interactions such as with xenoestrogens (to minimize inappropriate signaling and signaling deleterious to health) may be better controlled. The fractal approach is applied to analyte-ER interaction data available in the literature. Numerical values obtained for the binding and the dissociation rate coefficients are linked to the degree of roughness or heterogeneity (fractal dimension, D(f)) present on the biosensor chip surface. In general, the binding and the dissociation rate coefficients are very sensitive to the degree of heterogeneity on the surface. For example, the binding rate coefficient, k, exhibits a 4.60 order of dependence on the fractal dimension, D(f), for the binding of unliganded and liganded VDR mixed with GST-RXR in solution to Spp-1 VDRE (1,25-dihydroxyvitamin D(3) receptor element) DNA immobilized on a sensor chip surface (Cheskis and Freedman, Biochemistry 35 (1996) 3300-3318). A single-fractal analysis is adequate in some cases. In others (that exhibit complexities in the binding or the dissociation curves) a dual-fractal analysis is required to obtain a better fit. A predictive relationship is also presented for the ratio K(A)(=k/k(d)) as a function of the ratio of the fractal dimensions (D(f)/D(fd)). This has biomedical and environmental implications in that the dissociation and binding rate coefficients may be used to alleviate deleterious effects or enhance beneficial effects by selective modulation of the surface. The K(A) exhibits a 112-order dependence on the ratio of the fractal dimensions for the ligand effects on VDR-RXR interaction with specific DNA.

Biophysical Phenomena↗
PubMed2003

Caveats in the design of MHC class I tetramer/antigen-specific T lymphocytes dissociation assays.

Relative avidities of antigen-specific T cells for major histocompatibility complex peptide complexes (MHCp) have recently been measured by MHC tetramer dissociation assays, but there is no consensus on the methodologies used for these experiments. While we do not question the conclusions reached in previous studies, in this paper we discuss the caveats that are present in the design of all MHCp tetramer dissociation protocols, and we propose a set of criteria that should be met in the evaluation of appropriate methodologies. We find that it is necessary to use specific reagents to compete with rebinding of the labeled tetramer, but that when either intact anti-MHC antibodies or cold MHC tetramers are used, the dissociation rates are dependent upon the concentrations of the competitor. In contrast, we demonstrate that apparent dissociation rates are independent of the competitor concentration when blocking anti-MHC Fab fragments are used, suggesting that these are the most appropriate reagents to use for tetramer dissociation experiments.

Animals↗
PubMed1997

Determination of in situ dissociation constant for Fura-2 and quantitation of background fluorescence in astrocyte cell line U373-MG.

Accurate estimates of cytosolic free Ca2+ with fluorescence indicators are dependent on the determination of the in situ dissociation constants (kd) of the intracellular dyes and the correction for background fluorescence. The in situ dissociation constant for Ca2+ and indicator dye Fura-2/AM varies significantly from the in vitro published values due to differences in ionic strength, pH, viscosity and Ca2+ buffering by intracellular lipids and proteins. During the course of a measurement, background fluorescence changes may occur as the result of endogenous fluorescent compounds and compartmentalized Fura-2 indicator. The in situ dissociation constant value was determined for human astrocyte cell line U373-MG by creating several known intracellular Ca2+ concentrations while measuring total fluorescence and background fluorescence values for each. The background fluorescence was not constant, rather it demonstrated a linear relationship with the free cytosolic Ca2+ concentrations and total fluorescence intensities. The Ca2+ dependent and total fluorescence dependent background was expressed as a linear equation and subtracted appropriately from the total intensity measurements. The in situ dissociation constant was determined to be 3-fold greater than in vitro measurements after the background was corrected. The experimentally determined standard linear equations for background quantitation and the in situ dissociation constant for this line produce accurate cytosolic free Ca2+ estimates.

Astrocytoma↗
PubMed1997

Mechanisms of stabilizing nucleosome structure. Study of dissociation of histone octamer from DNA.

The influence of ionic strength on DNA-histone and histone-histone interactions in reconstituted nucleosomes was studied by measuring the parameters of histone tyrosine fluorescence: fluorescence intensity and lambda(max) position. The first parameter is sensitive to histone-DNA interactions. The changes of the second one accrue due to hydrogen bond formation/disruption between tyrosines in the histone H2A-H2B dimer and the (H3-H4)2 tetramer. The simultaneous measurement of these parameters permits the recording of both the dissociation of histone complexes from DNA, as well as changes in histone-histone interactions. As ionic strength is increased, the H2A-H2B histone dimer dissociated first, followed by dissociation of the (H3-H4)2 tetramer [Yager, T.G., McMurray, C.T. and Van Holde, K.E. (1989) Biochemistry 28, 2271-2276]. The H2A-H2B dimer is dissociated in two stages: first, the ionic bonds with DNA were disrupted, followed by the dissociation of the histone dimer from the tetramer. And secondly, the disruption of dimer-tetramer specific H-bonds. It was established that the energy of electrostatic interactions of the histone dimer with DNA within the nucleosome is much less than the energy of interaction of the histone dimer with the tetramer.

DNA↗
PubMed1998

Cold inactivation and dissociation into dimers of Escherichia coli tryptophanase and its W330F mutant form.

The kinetics and mechanism of reversible cold inactivation of the tetrameric enzyme tryptophanase have been studied. Cold inactivation is shown to occur slowly in the presence of K+ ions and much faster in their absence. The W330F mutant tryptophanase undergoes rapid cold inactivation even in the presence of K+ ions. In all cases the inactivation is accompanied by a decrease of the coenzyme 420-nm CD and absorption peaks and a shift of the latter peak to shorter wavelengths. The spectral changes and the NaBH4 test indicate that cooling of tryptophanase leads to breaking of the internal aldimine bond and release of the coenzyme. HPLC analysis showed that the ensuing apoenzyme dissociates into dimers. The dissociation depends on the nature and concentration of anions in the buffer solution. It readily occurs at low protein concentrations in the presence of salting-in anions Cl-, NO3- and I-, whereas salting-out anions, especially HPO4(2-), hinder the dissociation. K+ ions do not influence the dissociation of the apoenzyme, but partially protect holotryptophanase from cold inactivation. Thus, the two processes, cold inactivation of tryptophanase and dissociation of its apoform into dimers exhibit different dependencies on K+ ions and anions.

Bacterial Proteins↗
PubMed1996

On the dissociation and conformation of gas-phase methonium ions.

The dissociation pathways of both doubly and singly charged methonium ions, (CH(3))(3)N(+) -(CH(2))(n)-(+)N(CH(3))(3)·X(-) (n = 6,10; X = Br, I, and OAc), are measured using blackbody infrared radiative dissociation (BIRD) and SORI-CAD in a Fourier transform mass spectrometer. SORI-CAD of the doubly charged decamethonium ions results primarily in the formation of even electron ions by hydrogen rearrangements. In contrast, homolytic bond cleavage to form two odd electron ions is highly favored in the hexamethonium ion, presumably due to increased Coulomb repulsion in this ion. For BIRD of the singly charged salts, ions are mass selected and dissociated by heating the vacuum chamber to elevated temperatures. Under the low pressure conditions of our experiment, energy is transferred from the chamber walls to the ions by the absorption of blackbody radiation. From the temperature dependence of the unimolecular rate constants for dissociation, Arrhenius activation energies in the zero-pressure limit are obtained. The primary dissociation pathways correspond to counterion substitution reactions which result in loss of N(CH(3))(3) and CH(3)X. For hexamethonium and decamethonium with X = Br or I, the branching ratios for these pathways differ dramatically; the ratio of loss of N(CH(3))(3) and CH(3)Br is 3.8 and 0.4 for hexamethonium and decamethonium bromide, respectively. The hexamethonium acetate salt has a branching ratio of 0.1. The Arrhenius activation energies for hexamethonium (Br or I) and decamethonium (Br or I) are 0.9 and 1.0 eV, respectively. This value for hexamethonium acetate is 0.6 eV. Molecular dynamics simulations and Monte Carlo conformation searching are used to obtain the lowest energy structures of hexamethonium and decamethonium bromide. These calculations indicate that the methonium ion folds around the counterion to form a cyclic salt-bridge structure in which both quaternary nitrogens interact with the oppositely charged counterion. The significantly different branching ratios observed for these ions is attributed to the large change in orientation of the counterion with respect to the ammonium centers as the number of methylene groups in these ions increases. Similar ion conformational differences appear to explain the fragmentation for the OAc counter ion as well.

Journal Article↗
PubMed2003

A fractal analysis of analyte-estrogen receptor binding and dissociation kinetics using biosensors: environmental and biomedical effects.

A fractal analysis is used to model the binding and dissociation kinetics between analytes in solution and estrogen receptors (ERs) immobilized on a sensor chip of a surface plasmon resonance (SPR) biosensor. The influence of different ligands is also analyzed. A better understanding of the kinetics provides physical insights into the interactions, and suggests means by which appropriate interactions (to promote correct signaling) and inappropriate interactions such as with xenoestrogens (to minimize inappropriate and deleterious to health signaling) may be better controlled. The fractal approach is applied to analyte-ER interaction data available in the literature. The units for the different parameters (rate coefficients and affinities) in fractal-type kinetics are different from those obtained in classical kinetics. Numerical values obtained for the binding and the dissociation rate coefficients are linked to the degree of roughness or heterogeneity (fractal dimension, D(f)) present on the biosensor chip surface. In general, the binding and the dissociation rate coefficients are very sensitive to the degree of heterogeneity on the surface. A single-fractal analysis is adequate in some cases. In others (that exhibit complexities in the binding or the dissociation curves) a dual-fractal analysis is required to obtain a better fit. This has biomedical and environmental implications in that the dissociation (and the binding) rate coefficient may be used to alleviate (deleterious effects) or enhance (beneficial effects) by selective modulation of the surface. The affinity values obtained in the analysis are consistent with the numbers required to (a). promote signaling between the correct analyte and the estrogen receptor, and (b). minimize the signaling between xenoestrogens and the estrogen receptor.

Biomedical Technology↗
PubMed1997

Specificity of attachment and neurite outgrowth of dissociated basal forebrain cholinergic neurons seeded on to organotypic slice cultures of forebrain.

Development and differentiation of basal forebrain-derived cholinergic neurons were studied using a new technique that combines dissociated cell cultures with organotypic slice cultures. Slices of cerebral cortex or entire forebrain hemispheres were taken from early postnatal rat pups and maintained as organotypic cultures on membranes. Dissociated cell suspensions of basal forebrain tissue, taken from rat or mouse fetuses at gestational day 15-17, were seeded on to the slice cultures. Combined cultures were maintained for two to 14 days in vitro. Cultures processed for acetylcholinesterase histochemical staining demonstrated that stained neurons display regional variation in attachment to the slice, with most attachment occurring on cortex and with no detectable attachment on the caudate-putamen. Regional differences in attachment occur between cortical areas, with medial (cingulate) cortex showing much denser cell attachment than lateral (parietal) cortex, and across cortical layers, with layer I and deep layers showing more attachment than middle cortical layers. Similar patterns were observed on slices from rat brain irrespective of whether rat or mouse dissociated cells were used. Tyrosine hydroxylase-stained dissociated cells from ventral midbrain displayed a different pattern of attachment, with prominent attachment to the caudate putamen and less apparent specificity of regional and cortical laminar attachment. Little evidence of neurite outgrowth occurred during the first two days in vitro, but by four days, acetylcholinesterase-positive basal forebrain cells displayed several short and thick neurites that appeared to be dendrites, and one long process that appeared to be an axon. By seven days in vitro, dendrites are well developed and the presumed axon has extended branches over wide areas of cortex. These studies revealed several different types of cell-tissue interaction. The degree of cell growth and differentiation ranged from robust growth when dissociated cells were seeded on to slice cultures of normal target tissue, to apparently no attachment or growth when cells were seeded on to non-target tissue. This combined technique appears to be a useful method for studies of specificity of cell attachment and patterns of neurite outgrowth.

Acetylcholinesterase↗
PubMed2001

Collision-induced dissociation of bradykinin ions in the interface region of an ESI-MS.

By applying different electric field strengths to the orifice-skimmer region of an electrospray ionization mass spectrometer, the rate of dissociation can be varied based on the amount of internal energy acquired by an ion through collisions with the curtain gas molecules. Both the Arrhenius equation and Rice-Ramsperger-Kassel (RRK) theory can be used to predict the rate of dissociation of internally excited molecules. A previously determined model for collision-induced dissociation is tested by comparison of predicted and experimentally observed orifice-skimmer potential differences for dissociation of ions. The rate of collision-induced dissociation of bradykinin ions is determined by monitoring the fragments produced in a mass spectrometer. The semi-quantitative model is found to yield effective predictions when accurate Arrhenius and RRK parameters are utilized.

Algorithms↗
PubMed2001

Dissociation reactions of gaseous ferro-, ferri-, and apo-cytochrome c ions.

Electrochemical reduction of the iron bound in the heme group of cytochrome c is shown to occur in the nano-electrospray capillary if the protein is sprayed from neutral water using a steel wire as the electrical contact. Quadrupole ion trap collisional activation is used to study the dissociation reactions of cytochrome c as a function of the oxidation state of the iron. Oxidized (Fe(III)) cytochrome c dissociates via sequence-specific amide bond cleavage, while the reduced (Fe(II)) form of the protein dissociates almost exclusively by loss of protonated heme. Apo-cytochrome c, from which the heme has been removed either via gas-phase dissociation of the reduced holo-protein or via solution chemistry, dissociates via amide bond cleavage in similar fashion to the oxidized holo-protein.

Apoproteins↗
PubMed2002

A study of fast and metastable dissociations of adenine-thymine binary-base oligonucleotides by using positive-ion MALDI-TOF mass spectrometry.

In the present study, fast and metastable dissociations of a number of adenine-thymine binary-base oligonucleotides under the conditions of UV matrix-assisted laser desorption/ionization mass spectrometry were investigated. 2-Aminobenzoic acid/ammonium fluoride (ABA/NH4F) matrix system was used. The spectra obtained under metastable and fast dissociation conditions exhibit distinctive dissociation products. From the post-source-decay analysis, all oligonucleotides underwent predominantly metastable dissociations at the 3' C-O linkages to form [a(n)-B]+ and w(n)+ complimentary ion series. Based on the present results, the so-called "[wn+80]+" ions were postulated to be the complimentary [Z(8-n)AH]+ ions rather than the expected phosphate rearrangement products. In addition, these oligonucleotides were found to generate fast dissociation products of b(n)+, d(N)+, w(N)+ and y(N)+ ions through backbone cleavages at 5' C-O, 5' O-P, 3' C-O and 3' P-O linkages, respectively. Product ion series formed under PSD conditions were not observed. The implications of this mutually exclusive occurrence of the two sets of fragment ions under fast and metastable conditions using ABA/NH4F matrix would be discussed. A model of ion activation under UV-MALDI conditions was also proposed.

Adenine↗
PubMed1999

Determination of the dissociation kinetics of a transient intermediate.

Tandem mass spectrometry provides information on the dissociation pathways of gas-phase ions by providing a link between product ions and parent ions. However, there exists a distinct possibility that a parent ion does not dissociate directly to the observed product ion, but that the reaction proceeds through unobserved reaction intermediates. This work describes the discovery and kinetic analysis of an unobserved reaction intermediate with a quadrupole ion trap. [a4 - NH3] ions formed from [YG beta FL + H] ions dissociate to [(F*YG - NH3) - CO] ions. It is expected, however, from previous results, that [F*YG - NH3] ions should form prior to [(F*YG - NH3) - CO] ions. Double-resonance experiments are used to demonstrate the existence of intermediate [F*YG - NH3] ions. Various kinetic analyses are then performed using traditional collision-induced dissociation kinetics and double-resonance experiments. The phenomenological rates of formation and decay of peptide rearrangement ion dissociation products are determined by curve fitting decay and formation data generated with the kinetics experiments. The data generated predict an observable level of the intermediate in a time frame accessible but previously not monitored. By examining early product-ion formation, the intermediate ions, [F*YG - NH3]+, are observed.

Kinetics↗
PubMed2000

An electrospray-ionization mass spectrometry analysis of the pH-dependent dissociation and denaturation processes of a heterodimeric protein.

Electrospray ionization mass spectrometry (ESI-MS) was applied to the analysis of the dissociation and denaturation processes of a heterodimeric yeast killer toxin SMKT. The two distinct subunits of SMKT noncovalently associate under acidic conditions, but become dissociated and denatured under neutral and basic conditions. In order to understand the unique pH-dependent denaturation mechanism of this protein, a pH titration was performed by utilizing ESI-MS. The molecular ions of the heterodimer which possesses the highly ordered structure, were mainly observed below pH 4.6. However, the two subunits immediately dissociated at this pH. The spectra measured with various settings of the mass spectrometer indirectly demonstrated that the pH-dependent dissociation occurs in the liquid phase. The current result as well as the three-dimensional structure of SMKT suggest that the deprotonation of a specific carboxyl group triggers a cooperative dissociation process of this protein. In conclusion, the pH titration of a protein by ESI-MS is particularly effective, when the unfolding process or the biological function of the protein is related to the interaction with other molecules.

Fungal Proteins↗