Characteristics of sulfhydryl groups of histone H3 from the calf thymus using mercury-containing nitroxyl radicals

The interaction between total histone and deoxyribonucleoprotein (DNP) preparations from calf thymus with mercury-containing nitroxyl radicals in low ionic strength solutions, 2 M NaCl and urea was investigated. It was found that the label is rapidly incorporated into the SH-groups of histone H3 to produce characteristic EPR signals. Titration of SH-groups within DNP demonstrated that in low ionic strength solutions only one SH-group (presumably, the SH-group of the cysteine residue in position 110) is accessible to the reagents. After dissociation by 2 M NaCl, two SH-groups become titrable; however, the EPR spectra point to differences in the conformational state of these two groups. In 4 M urea, these differences are compensated for by structural disintegration. The spin labels may be used for the analysis of SH-groups under different conditions and at different functional states of nucleoproteins.     

A kinetic study of the reactive capabilities of xanthine oxidase sulfhydryl groups with regard to n-chlormercuribenzoate]

Kinetic characteristics for reactivity of SH-groups of milk xanthine oxidase were obtained under different conditions. Two types of SH-groups with rate constant values, differing by a factor of about 50, were found in a phosphate buffer at pH 7.0. The slow stage of reaction is followed by protein precipitation. The number of fast- (12) and slowly-reacting (60) groups were calculated from the kinetic data. The blocking of the fast-reacting groups occurs without loss of the enzyme activity. The values of activation energy for the fast- and slowly-reacting groups are 15 and 48 kcal/mol respectively. The formation of the enzyme-substrate complex stabilizes the enzyme molecule; the number of fast-reacting SH-groups and the rate constant values for both types of groups remain unchanged, whereas the number of slowly-reacting SH-groups markedly decreases (37). The values of activation energy for both types of SH-groups show no changes in the presence of substrate. Conformations of the enzyme in different denaturating solvents were characterized by a number of SH-groups, reacting with p-chloromercurybenzoate. 54 groups are exposed in solutions of groups exposed in 7.0-8.5 M urea solutions is 35-38. In all solvents studied the protein molecule is probably not completely unfolded, since the number of exposed SH-groups is less than the full number of SH-groups determined by the amino acid analysis. Only 42 SH-groups reacted with 5,5'-dithiobis-(2-nitrobenzoic acid) under the same conditions.     

The content and types of sulfhydryl groups in muscle creatine kinase detected by their accessibility to different reagents

Using three independent methods tte amperometric titration, Boyer's method and the method of Ellman it is shown that rabbit muscle creatine kinase contains 11-12 SH-groups, 3-6 of which are easily oxidized by atmospheric oxygen to form S-S-bonds. It is found that creatine kinase has four types of SH-groups distinguished by their accessibility to different SH-reagents. The first type related to the enzymatic activity is detected by the Ellman method (2 SH-groups), the first and the second ones taken together--by the Boyer method (4 SH-groups), the first, second and third ones--by the method of amperometric titration (6 SH-groups), all the 4 types together--when detecting SH-groups after protein denaturation--by any of the above methods (8-12 SH-groups).     

Four free cysteine residues found in human IgG1 of healthy donors

Modifications with different thiol reagents demonstrated that 28 of 32 cysteine residues of human IgG1 are involved in the formation of disulfide bonds, and four cysteines remain free. So IgG1 is a protein possessing both free SH-groups and disulfide bonds. Only one of the four SH-groups is accessible for silver or mercury ions and hydrophobic reagents, whereas the remaining three SH-groups are masked and can be revealed only after deep denaturation of the protein. Detection of the masked cysteine residues was shown to depend on the kinetics of intramolecular changes occurring during denaturation of the protein and on the method of the assay of the SH-groups.     

Copper (II) Ions Affect <Emphasis Type="Italic">Escherichia coli</Emphasis> Membrane Vesicles’ SH-Groups and a Disulfide-Dithiol Interchange Between Membrane Proteins

The SH-groups in Escherichia coli membrane vesicles, prepared from cells grown in fermentation conditions on glucose at slightly alkaline pH, have a role in the F0F1-ATPase operation. The changes in the number of these groups by ATP are observed under certain conditions. In this study, copper ions (Cu2+) in concentration of 0.1 mM were shown to increase the number of SH-groups in 1.5- to 1.6-fold independent from K+ ions, and the suppression of the increased level of SH-groups by ATP was determined for Cu2+ in the presence of K+. Moreover, the increase in the number of SH-groups by Cu2+ was absent as well as the inhibition in ATP-dependent increasing SH-groups number by Cu2+ lacked when vesicles were treated with N-ethylmaleimide (NEM), specific thiol-reagent. Such an effect was not observed with zinc (Zn2+), cobalt (Co2+), or Cu+ ions. The increased level of SH-groups was observed in the hycE or hyfR mutants with defects in hydrogenases 3 or 4, whereas the ATP-dependent increase in the number of these groups was determined in hycE not in hyfR mutants. Both changes in SH-groups number disappeared in the atp or hyc mutants deleted for the F0F1-ATPase or hydrogenase 3 (no activity of hydrogenase 4 was detected in the hyc mutant used). A direct effect of Cu2+ but not Cu+ on the F0F1-ATPase is suggested to lead to conformational changes or damaging consequences, increasing accessible SH-groups number and disturbing disulfide-dithiol interchange within a protein-protein complex, where this ATPase works with K+ uptake system or hydrogenase 4 (Hyd-4); breaks in disulfides are not ruled out.     

Mechanical and Electrical Oscillations in Cardiac Muscle of the Turtle

During contractures of the turtle ventricle rapid changes in length induce sinusoidal oscillations under isotonic conditions. They are due to delayed responses to stretching and release, which can be demonstrated also under isometric conditions. Oscillations of two distinct frequencies are produced under different conditions and are distinguished as high- and low-frequency oscillations. In depolarized muscles the frequency is such that the duration of one cycle is about the same as that of a normal twitch, while in high-Ca solutions the duration can be the same as in high-K solutions or about six times lower. As reported previously, twitches are followed by weak mechanical and electrical oscillations. Their frequency agrees with the high-frequency oscillations. The same effects can also be induced by stretching and release. It is suggested that the phenomena observed are due to feedback mechanisms which originate in the contractile mechanism. The high-frequency oscillations are similar to those observed previously in other muscles, particularly insect fibrillar muscle, and are not due to changes in Ca concentration. The other mechanisms involve the membrane and possibly the intracellular Ca stores.     

Content of SH-groups in some fractions of rat hemoglobin

Eight fractions of rat hemoglobin obtained by electrophoresis in polyacrylamide gel were studied. Having used parachloromercuric benzoate (PChMB) and 5,5-dithio-bis (2-nitrobenzoic acid) it was established that fractions of 3 and 3a carboxyhemoglobin contain 6 available SH-groups and the rest one (1, 2, 2a, 4, 5, 6) about 4 SH-groups. In all fractions only 2 masked SH-groups are found. A problem is discussed on SH-groups localization in the polypeptide chains of certain hemoglobin fractions in rats.     

Effect of oligomerization on the properties of essential SH-groups of mitochondrial creatine kinase

The properties of creatine kinase isolated from bovine heart mitochondria in dimeric (Mr = 84 +/- 6 kD) and octameric (Mr = 340 +/- 17 kD) forms were compared with those of the earlier described hexameric form of the enzyme (Mr = 240 +/- 12 kD). The kinetics of SH-group modification by DTNB, the inactivation kinetics as well as the number of modified SH-groups point to significant differences between the three oligomeric forms of the enzyme. Each subunit of creatine kinase was found to possess one "fast" essential cysteine residue whose modification by DTNB and iodoacetamide led to enzyme inactivation. The formation of an analog of the transition state complex (E--MgADP--NO3--creatine) was paralleled with partial protection of only the "fast" cysteine residue which manifested itself in the decrease of the rate of its interaction with DTNB in all the three oligomeric forms. Dimer association into a hexamer and octamer occurred in parallel with a decrease of the affinity of essential SH-groups of cysteine for DTNB in 50% of the oligomeric molecule subunits. Thus, in the dimer two essential SH-groups were rapidly modified by DTNB at the same rate: k1 = k2 = (23.9 +/- 5.6).10(4) M-1 min-1. Within the hexamer, the rate of modification of 3 out of 6 SH-groups was practically unchanged: k1 = (10.6 +/- 2.3).10(4) M-1 min-1. Another 3 SH-groups in the remaining 50% of the subunits were partly masked, which manifested itself in a 10-fold decrease of their modification rate: k2 = (1.12 +/- 0.28).10(4) M-1 min-1. Within the octamer, the SH-groups rapidly interacted with DTNB only on 4 subunits: k1 = (20.7 +/- 2.2).10(4) M-1 min-1, whereas in the remaining 4 octamer subunits a practically complete masking of essential SH-groups was observed, as a result of which these groups became inaccessible to DTNB. This manifested itself in a 1000-fold decrease of the rate of SH-group modification by DTNB which reached that of non-essential SH-group modification. In has been found that a complete loss of the octamer activity is due to the modification of only 4 SH-groups which interact with DTNB at a high rate. A model for subunit association into a dimer, hexamer and octamer has been proposed. Presumably, 50% of the active centers in the mitochondrial creatine kinase octamer are not involved in the catalytic act.     

Study of reactivity of sulfhydryl groups of troponin]

The reactivities of SH-groups of troponin and its components were studied, using 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl). At low concentrations of Ca2+ (pCa greater than 8) one rapidly- and two slowly-reacting SH-groups of troponin I and one SH-group of troponin C slowly reacting with NBD-chloride are titrated in the whole troponin complex. When Ca2+ concentration is increased up to pCa less than 5, only one slowly-reacting and one rapidly-reacting with NBD-chloride SH-groups of troponin I are titrated. The increase of Ca2+ concentration from pCa greater than 8 to pCa less than 5 results in a change of the environment polarity for the highly reactive SH-group of troponin I in the whole troponin complex. This phenomenon may suggest that the changes in troponin C structure during Ca2+ binding somehow induce changes in that of troponin I. The half-maximal change of troponin SH-groups reactivity is found at pCa 6.8. No cooperativity for Ca2+ binding by the troponin complex is observed using SH-groups titration by NBD-Cl.     

Histological and histochemical studies of the male reproductive system of Ligia exotica Roux (Crustacea: Isopoda)

The male reproductive system of Ligia exotica consists of a pair of testes, a pair of vasa deferentia and a pair of genital pores. The testes are tube-like, unpigmented and translucent and each is composed of three elongate, fusiform follicles. The follicular lumen of the mature testis contains spermatogonia, spermatocytes, spermatids and spermatozoa. The histochemical reactions of the testis and the vas deferens show the presence of acidic sulphated mucopolysaccharides and neutral mucopolysaccharides. In addition, they contain basic proteins, tyrosine, disulphide groups, SH-groups, SH-groups, lipids, phospholipids, RNA and DNA.     

Hysteresis phenomena between periodic and stationary solutions in a model of pacemaker and nonpacemaker coupled cardiac cells

We were interested in investigating the behaviour of a cardiac electrophysiological model including coupled pacemaker (PM) and nonpacemaker (NPM) cells. To this aim, a modified version of the model of Van Capelle and Durrer was used. First, few discrete values were assigned to coupling resistance (CR) and respective cell sizes and numerical simulations versus time showed three possible kinds of response pattern: sustained rhythmic activity, subthreshold oscillations, and complete inhibition. Then, after setting a fixed value to PM cell size, we undertake a thorough study of the system by using bifurcation-continuation techniques and CR was chosen as the continuation parameter. On the maximum action potential — CR plane representation, we could describe five behavioural zones: complete inhibition, coexistence of complete inhibition and NPM large oscillations, NPM large oscillations, coexistence of NPM large oscillations and subthreshold oscillations, subthreshold oscillations. Within the zones of qualitatively different coexisting solutions, a detailed exploration clearly demonstrated the presence of hysteresis cycles. Indeed, the status of the system depended on its immediate previous story within narrow ranges of CR values. Such a coexistence of stable solutions for identical values of CR may suggest an explanation of the intermittant activity elicited from abnormal ectopic foci observed in certain ventricular rhythm disturbances. In addition, a Hopf bifurcation point, from which emerged stationary and periodic solutions, was followed on the PM cell size — CR plane and from this representation we could deduce that the smaller the PM cell, the higher the CR must be for the PM cell to escape from the NPM cell inhibition.     

Non-equivalency of SH groups essential for the activity of mitochondrial creatine kinase

The properties of SH-groups of mitochondrial creatine kinase existing in solution as a hexamer with Mr of (240 +/- 12) X 10(3) Da, were investigated. The number and reactivity of SH-groups by specific modifiers--[5.5'-dithiobis-(2-nitrobenzoic acid), DTNB; 7-chloro-4-nitrobenzo-2-oxo-1.3-diazol, NBD-Cl; 2.2'-dithiopyridine, DTP] were determined. It was found that each subunit of the enzyme hexameric molecule contains two modified SH-groups, only one of which is protected against modification by Mg-ADP, Mg-ATP as well as during the formation of the transition state analog (TSA)--E-Mg X ADP-NO3-creatine--and is essential for the enzyme activity. These six essential SH-groups within the hexameric molecule of mitochondrial creatine kinase may be classified into two groups according to the rate of their interaction with DTNB, NBD-Cl and DTP. The rate constants of modification of three fast and three slow essential SH-groups differ 4-10 times. The kinetics of enzyme inactivation by iodoacetamide (IAA) is biphasic; each phase is characterized by a 50% loss of activity. The inactivation constants differ 30 times; both phases being protected by TSA; consequently, the inactivation is caused by the binding of IAA to the essential SH-groups. The unequal reactivity of essential SH-groups seems to be preexisting. Using a computer analysis, the dependence of the amount of residual activity on the number of modified SH-groups by NBD-Cl and DTNB was studied. The interaction of NBD-Cl and DTNB with the most reactive essential SH-groups in half of the subunits results in the inactivation of these subunits as well as in partial or complete inactivation of the other half of the non-modified subunits. The degree of inactivation of the latter 50% of subunits strongly depends on the nature of the modifier. The inactivating effect of the bound modifier is translated from one subunit to another in one direction. The experimental results point to asymmetrical association of mitochondrial creatine kinase subunits.     

Transient oscillations induced by delayed growth response in the chemostat

In this paper, in order to try to account for the transient oscillations observed in chemostat experiments, we consider a model of single species growth in a chemostat that involves delayed growth response. The time delay models the lag involved in the nutrient conversion process. Both monotone response functions and nonmonotone response functions are considered. The nonmonotone response function models the inhibitory effects of growth response of certain nutrients when concentrations are too high. By applying local and global Hopf bifurcation theorems, we prove that the model has unstable periodic solutions that bifurcate from unstable nonnegative equilibria as the parameter measuring the delay passes through certain critical values and that these local periodic solutions can persist, even if the delay parameter moves far from the critical (local) bifurcation values.When there are two positive equilibria, then positive periodic solutions can exist. When there is a unique positive equilibrium, the model does not have positive periodic oscillations and the unique positive equilibrium is globally asymptotically stable. However, the model can have periodic solutions that change sign. Although these solutions are not biologically meaningful, provided the initial data starts close enough to the unstable manifold of one of these periodic solutions they may still help to account for the transient oscillations that have been frequently observed in chemostat experiments. Numerical simulations are provided to illustrate that the model has varying degrees of transient oscillatory behaviour that can be controlled by the choice of the initial data.Mathematics Subject Classification: 34D20, 34K20, 92D25Research was partially supported by NSERC of Canada.This work was partly done while this author was a postdoc at McMaster.     

Steady states and outbreaks of two-phase nonlinear age-structured model of population dynamics with discrete time delay

In this paper we study the nonlinear age-structured model of a polycyclic two-phase population dynamics including delayed effect of population density growth on the mortality. Both phases are modelled as a system of initial boundary values problem for semi-linear transport equation with delay and initial problem for nonlinear delay ODE. The obtained system is studied both theoretically and numerically. Three different regimes of population dynamics for asymptotically stable states of autonomous systems are obtained in numerical experiments for the different initial values of population density. The quasi-periodical travelling wave solutions are studied numerically for the autonomous system with the different values of time delays and for the system with oscillating death rate and birth modulus. In both cases it is observed three types of travelling wave solutions: harmonic oscillations, pulse sequence and single pulse.     

The role of cysteinyl residues in the phosphorylase kinase activity as revealed by iodacetamide modification

In native nonactivated phosphorylase kinase [14C] iodacetamide interacts with 50 cysteinyl residues per enzyme molecule (alpha beta gamma delta)4. According to their reactivity towards iodacetamide these residues can be classified into 3 groups. The most reactive cysteinyl residues are involved in the enzyme activation caused by modification of SH-groups. The enzyme inhibition is biphasic. The fast and slow inactivation reactions follow the pseudo-first order kinetics. The rate of inactivation is increased by Ca2+. Mg-ATP effectively protects the enzyme against the inactivation and chemical modification of three SH-groups per protomer (apha beta gamma delta). The kinetics of inactivation and of the [14C] iodacetamide label incorporation demonstrate that two cysteinyl residues per enzyme protomer (alpha beta gamma delta) are essential for the enzyme activity. These residues are located near the ATP-binding site of the beta and gamma subunits of phosphorylase kinase.     

Localization of a new proteolytic site accessible in oxidized myosin rod

We have compared the proteolysis pattern of reduced and oxidized myosin rods in which the five pairs of SH-groups were interchain crosslinked by employing CuCl2 or 5,5'-dithiobis-2-nitrobenzoate. In the tryptic digest of oxidized rod three new fragments appeared on SDS-polyacrylamide gel electrophoresis (chain masses of 100, 45, and 25 kDa). Based on the N-terminal sequences of the isolated peptides, it is concluded that oxidation creates a new cleavage site 102 residues away from the N-terminus of the rod, in the vicinity of one of the modified SH-groups (Cys-108). This observation indicates that S-S crosslinking of myosin rod leads to a local unfolding of the coiled-coil structure.     

Study on the role of SH-groups in the activity of muscle pyruvate dehydrogenase

The kinetics of inactivation of the pyruvate dehydrogenase component of the pigeon breast muscle pyruvate dehydrogenase complex in the presence of 5,5'-dithiobis (2-nitrobenzoate) is biphasic. The rate constants for the fast and slow phases of the inactivation reaction are close to those for modification of two classes of SH-groups differing in their reactivities towards the inhibitor. The reaction order with respect to the inhibitor concentration suggests that the two distinct SH-groups are essential for the enzyme activity. Modification of these SH-groups results in inhibition of the overall activity of the pyruvate dehydrogenase complex and of the 2-hydroxyethyl thiamine pyrophosphate - acceptor oxidoreductase activity of its decarboxylating component. Thiamine pyrophosphate exerts a protective effect on the enzyme only at the slow phase of the enzyme inactivation and SH-modification. As a result of interaction between the holoenzyme and pyruvate (or apoenzyme and 2-hydroxyethyl thiamine pyrophosphate) the rate of the enzyme inactivation is increased. This is associated with masking of non-essential SH-groups and with an increase of the accessibility of two essential SH-groups to the inhibitor. The data obtained suggest the interrelationship between the essential SH-groups and the 2-hydroxyethyl thiamine pyrophosphate-acceptor oxidoreductase activity of pyruvate dehydrogenase.     

Structural observations of time dependent oscillatory behavior of CuIICl2 solutions measured via extended X-ray absorption fine structure

Cell surface ECTO-NOX proteins exhibit a clock-related, temperature-independent entrainable pattern of periodic (24 min) oscillations in the rate of oxidation of NAD(P)H. Aqueous solutions of copper salts also oxidize NAD(P)H with a similar temperature-independent pattern. For both, five maxima are observed, two of which are separated by 6 min and the remaining three are separated by 4.5 min. In D2O, the pattern is retained but the period length is proportionately increased to 30 min in direct relationship to the 30 h circadian day observed with D2O-grown organisms. With copper solutions, periodic changes in redox potential correlate precisely with the periodic changes in the rates of NAD(P)H oxidation. Consequently, the local environment of the Cu2+ ion in copper chloride solutions was investigated by X-ray absorption spectroscopy. Detailed extended X-ray absorption fine structure (EXAFS) analyses revealed a pattern of oscillations closely resembling those of the copper-catalyzed oxidation of NADH. With CuCl2 in D2O, a pattern with a period length of 30 min was observed. The findings suggest a regular pattern of distortion in the axial and/or equatorial oxygen atoms of the coordinated water molecules which correlate with redox potential changes sufficient to oxidize NADH. A metastable equilibrium condition in the ratio of ortho to para nuclear spin orientation of the water associated hydrogen atoms would be kinetically consistent with a 24-30 min timeframe. The temperature independence of the biological clock can thus be understood as the consequence of a physical rather than a chemical basis for the timing events.     

The mechanism of photodamage of eye structures. IV. Changes in the reactivity of crystalline SH-groups during UV irradiation

The kinetics of individual crystalline SH-group modification by DTNB were studied. According to the rates of their interaction with the modifier, the thiol groups in the native protein molecule can be classified as free, accessible, weakly modified and "masked" ones. Denaturation by the detergent (CTAB) caused an increase in the SH-group modification rate. In this case the SH-groups were modified as free and accessible ones. Illumination with UV-light resulted in a decrease in the number of SH-groups, opening of "masked" SH-groups in almost all crystallines except for alpha-crystalline, and essential changes in the SH-group modification rate.     

Roles of protein ubiquitination and degradation kinetics in biological oscillations

Protein ubiquitination and degradation play important roles in many biological functions and are associated with many human diseases. It is well known that for biochemical oscillations to occur, proper degradation rates of the participating proteins are needed. In most mathematical models of biochemical reactions, linear degradation kinetics has been used. However, the degradation kinetics in real systems may be nonlinear, and how nonlinear degradation kinetics affects biological oscillations are not well understood. In this study, we first develop a biochemical reaction model of protein ubiquitination and degradation and calculate the degradation rate against the concentration of the free substrate. We show that the protein degradation kinetics mainly follows the Michaelis-Menten formulation with a time delay caused by ubiquitination and deubiquitination. We then study analytically how the Michaelis-Menten degradation kinetics affects the instabilities that lead to oscillations using three generic oscillation models: 1) a positive feedback mediated oscillator; 2) a positive-plus-negative feedback mediated oscillator; and 3) a negative feedback mediated oscillator. In all three cases, nonlinear degradation kinetics promotes oscillations, especially for the negative feedback mediated oscillator, resulting in much larger oscillation amplitudes and slower frequencies than those observed with linear kinetics. However, the time delay due to protein ubiquitination and deubiquitination generally suppresses oscillations, reducing the amplitude and increasing the frequency of the oscillations. These theoretical analyses provide mechanistic insights into the effects of specific proteins in the ubiquitination-proteasome system on biological oscillations.