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Biomedical subjects

A A Alexandrov

Publications and source records attributed to A A Alexandrov.

At least 19 recordsLinked to original sources

Mathematical modeling of living cell metabolism using the method of steady-state stoichiometric flux balance.

This approach uses a set of algebraic linear equations for reaction rates (the method of steady-state stoichiometric flux balance) to model the purposeful metabolism of the living self-reproducing biochemical system (i.e. cell), which persists in steady-state growth. Linear programming (SIMPLEX method) is used to derive the solution for the model equations set (determining reaction rates which provide flux balance at given conditions). Here, we demonstrate the approach through the mathematical modeling of steady-state metabolism in Saccharomyces cerevisiae mitochondria.

Algorithms↗

Role of the electrostatic interactions in pre-orientation of subunits in the formation of protein-protein complexes.

Theoretical estimation of contribution of the electrostatic interactions to pre-orientation of ribonuclease subunits in process of complex formation was carried out. The subunit was considered as a multipole consisting of partial charges of all atoms of the molecule. The object of investigation was a system of two subunits with their centers of gravity fixed at some distance in vacuum. It was proposed that each subunit independently could rotate freely around its fixed center of gravity. The relative orientation states of the subunits in such system were searched at which the system has electrostatic energy minima (equilibrium states). In first approximation the equilibrium states were found using especially designed approximate method for electrostatic interaction energy calculation, which permitted to calculate and compare the energies of the system in 24(5) (approximately 8 10(6)) states with different mutual orientation of subunits. The angular coordinates of the found equilibrium states were further specified by calculation with gradient sliding method. Angular coordinates of the equilibrium states and the shapes of energy surface cuts along each coordinate angle were calculated also for the intersubunits distances diminished down to 50 angstroms. The dispersions of the angular coordinates of equilibrium states caused by heat movement (at T=300 degrees) and their changes with shortening the distance between centers of gravity of subunits were estimated. Mutual orientation of subunits in the equilibrium states of the system under consideration was found to be similar to their mutual orientations in complex. Also it was found that relaxation time of the system, caused by electrostatic interaction of subunits, after removing the system from an equilibrium state, is much less in vacuum than the mean time between their Brownian collisions at room temperature. It follows from these results that in the case of ribonuclease in vacuum the electrostatic interactions of its subunits must be strong enough to realize the effective pre-orientation of subunits during their Brownian approach from distances of the order 100 angstroms. Preliminary consideration taking into account the effect of surrounding water molecules on the electrostatic interactions of ribonuclease subunits showed that weakening of the interaction must be much less than in the case when one uses in its calculation the macroscopic dielectric permeability value equal to 80. So the results obtained for vacuum seem to be true for water solution also. More strict theoretical analysis of this problem will be carried out in the following publication.

Animals↗

About factors providing the fast protein-protein recognition in processes of complex formation.

A package of programs for the examination of areas of subunit contacts (interface) in protein-protein (PP) complexes has been created and used for a detailed study of amino acid (AA) composition and interface structure in a large number of PP complexes from Brookhaven database (PBD). It appeared that in about 75% of the complexes, the AA composition of the subunit surface is not important. This suggests that, along with the surface AA composition, interactions between AA from the inner parts of protein globules may play a significant role in PP recognition. Such interactions between relatively distant AA residues can only be of electrostatic nature and contribute to the total electric field of the protein molecule. The configuration of the electric field itself appears to determine the PP recognition. The total electric field created by protein molecules can be calculated as a result of superimposition of the fields created by the protein multipole (i.e. by the totality of partial electric charges assigned to each atom of the molecule). We performed preliminary calculations for the distant electrostatic interaction of ribonuclease subunits in a vacuum. The results reveal that the effect of the electric fields of the protein multipole is strong enough to orient protein molecules prior to their Brown collision.

Amino Acids↗

Cytochrome P450 pattern revision.

The pattern suggested for the structure-function superfamily of cytochromes P450 is composed by combining the conserved amino acid motifs. The sizes of P450 cytochromes were estimated according to their length. The empirical coefficients reflecting the peculiarities of the primary structure of these enzymes are calculated. We propose an approach for determining novel proteins sequences to the mentioned superfamily on the ground of the complex of these parameters. A number of the hypothetical proteins from the international databases is related to the cytochromes P450 by means of our pattern.

Amino Acid Sequence↗

Molecular mechanisms of protein-protein recognition: whether the surface placed charged residues determine the recognition process?

We studied the structure and composition of contact areas in 812 different kind dimeric protein-protein complexes from Brookhaven data base (PDB ) in order to reveal their pecularities with regard to protein-protein recognition. We have found, that the large portion of complexes (approximately 70%) have oppositely charged residues in the contact areas (interfaces) on the subunits surfaces, which form electrostatic contacts - R:E, R:D, K:E, K:D, H:E, H:D. These results are consistent with the current view that high rate complex formation may be driven by the long-range electrostatic interaction between charged AA residues of subunits surfaces. However, there are many complexes among the studied ones (approximately 30%), which have no electrostatic contacts at all in their contact area. Thus a question arises: what forces account for high complex formation rates (i.e. for the distant orienting of subunits before encounter) by forming complexes where the surface contact areas lack electrostatic contacts? We believe that the long-range orienting electrostatic interaction of subunits may account for all cases of efficient complex formation if one drops the traditional view that protein subunits interact mainly through their surfaces. We suggest that the distant orienting being due to the electrostatic interaction between the whole aggregates of partial electric charges of atoms of each complex subunits. Our preliminary model calculations (unpublished) made for ribonuclease dimer (does not have electrostatic contacts) conform this suggestion.

Binding Sites↗

Hypothetical 92.3-kD human protein homologous to angiotensin-converting enzyme: a new member of the zinc metalloprotease family?

Significant identity between a hypothetical 92.3-kD human protein and angiotensin-converting enzyme (ACE; peptidyl-dipeptidase A; kininase II) has been found. Certain specific regions of the 92.3-kD protein indicate that this unidentified molecule may be a member of the zinc metalloprotease family. A method is suggested for determination of a structural and functional family of proteins with unknown structure and function.

Amino Acid Motifs↗

The enzyme activity allosteric regulation model based on the composite nature of catalytic and regulatory sites concept.

A new kinetic model of enzymatic catalysis is proposed, which postulates that enzyme solutions are equilibrium systems of oligomers differing in the number of subunits and in the mode of their assembly. It is suggested that the catalytic and regulatory sites of allosteric enzymes are of composite nature and appear as a result of subunits joining. Two possible joining modes are postulated at each oligomerization step. Catalytic site may arise on oligomer formed only by one of these modes. Effector acts by fastening together components of certain oligomeric form and increases the life time of this form. It leads to a shift of oligomer equilibrium and increases a proportion of effector-binding oligomers. Effectors-activators bind the oligomers carrying composite catalytic sites and effectors-inhibitors bind the oligomers, which do not carry active catalytic sites. Thus, catalytic activity control in such system is explained by effector-induced changes of a catalytic sites number, but not of a catalytic site activity caused by changes of subunit's tertiary structure. The postulates of the model do not contradict available experimental data and lead to a new type of general rate equation, which allows to describe and understand the specific kinetic behavior of allosteric enzymes as well as Michaelis type enzymes. All known rate equations of allosteric The equation was tested by modeling the kinetics of human erythrocyte phosphofructokinase. It enabled to reproduce quantitatively the 66 kinetic curves experimentally obtained for this enzyme under different reaction conditions.

Allosteric Regulation↗

Small circles of helical DNA obtained on the basis of transcriptional pause sites sequence.

The 21-base pair synthetic DNA duplexes with basic 'pause-motif site ('CATGC') were ligated head-to-tail to produce linear and circular multimers. This also was done from other closely related sequences. Electrophoretic mobilities of the linear multimers in polyacrylamide gels were determined under the standard and modified conditions. We revealed that small linear multimers (approximately 90 bp) were characterized by comparable value of gel retardation relative to the well known curved DNA, while longer multimers (130 to approximately 170 bp) had only slightly expressed mobility anomaly. Nevertheless these multimers containing nontruncated 'pause-motif were capable of cyclization, in particular, formation of unusually small circles while truncated ones were not. We conclude that basic 'pause-motif site increases the closure ability while the multimers based on truncated 'pause motif fail to curve into the small circles. We tend to explain this situation as a result of intrinsic bending as well as the influence of the thermal fluctuations of DNA, the latter most probably can be associated with 'pause motif'. We have estimated the equilibrial and maximal bend angles per 10.5 bp to be 12 degrees to approximately 16 degrees and 32 degrees accordingly under experimental conditions of our study.

Binding Sites↗

Comparison of attitudes and behaviors related to nutrition, body size, dieting, and hunger in Russian, black-American, and white-American adolescents.

Attitudes and behaviors related to nutrition are known to differ between white-American and black-American adolescents, however, little is known about teenagers from Russia. We hypothesized that, compared with white-American or black-American teenagers, Russian teenagers would prefer a larger body size, be less likely to diet, and be less concerned about being overweight. Self-administered questionnaires were completed by 196 students in Moscow, 326 white-American, and 239 black-American adolescents who attended school in North Carolina (mean age = 16). Ideal body mass index (BMI) was calculated from measured height and the response to the question, "What do you consider to be your ideal weight?" Mean ideal BMI was higher in black-American boys (25.1) and girls (21.4) than in white-American boys (22.1) and girls (19.2), and Russian boys (21.8) and girls (19.1). After controlling for BMI, black-American girls were less than half as likely to report dieting compared with white-American girls. There were no significant differences among white-American girls and Russian girls, and there were no ethnic differences between boys in the prevalence of dieting. White-American girls and black-American girls were much more likely to identify being overweight as an important nutritional concern than were Russian girls (odds ratios > 10), and there were no ethnic differences among boys. We conclude that preferences for body size, the prevalence of dieting, and concerns about being overweight were similar in Russian and white-American teens, with the exception of Russian teenaged girls who were less likely than American girls to identify being overweight as an important concern. Overall, weight-related attitudes and behaviors in Russian teenagers were more similar to those of white-American teenagers than those of black-American teenagers.

Adolescent↗

D2O-induced ion channel activation in Characeae at low ionic strength.

Effects of D2O were studied on internodal cells of the freshwater alga Nitellopsis obtusa under plasmalemma perfusion (tonoplast-free cells) with voltage clamp, and on Ca2+ channels isolated from the alga and reconstituted in bilayer lipid membranes (BLM). External application of artificial pond water (APW) with D2O as the solvent to the perfused plasmalemma preparation led to an abrupt drop of membrane resistance (Rm = 0.12 +/- 0.03 k omega.cm2), thus preventing further voltage clamping. APW with 25% D2O caused a two-step reduction of Rm: first, down to 2.0 +/- 0.8 k omega.cm2, and then further to 200 omega.cm2, in 2 min. It was shown that in the first stage, Ca2+ channels are activated, and then, Ca2+ ions entering through them activate the Cl- channels. The Ca2+ channels are activated irreversibly. If 100 mM CsCl was substituted for 200 mM sucrose (introduced for iso-osmoticity), no effect of D2O on Rm was observed. Intracellular H2O/D2O substitution also did not change Rm. In experiments on single Ca2+ channels in BLM H2O/D2O substitution in a solution containing 100 mM KCl (trans side) produced no effect on channel activity, while in 10 mM KCl, at negative voltage, the open channel probability sharply increased. This effect was irreversible. The single channel conductance was not altered after the H2O/D2O substitution. The discussion of the possible mechanism of D2O action on Ca2+ and Cl- channels was based on an osmotic-like stress effect and the phenomenon of higher D-bond energy compared to the H-bond.

Calcium Channels↗

Primary prevention of cardiovascular disease: 3-year intervention results in boys of 12 years of age.

BACKGROUND: The intervention group comprised 477 children at the age of 11.8 +/- 0.11 years. The reference group comprised 528 children aged 11.9 +/- 0.12 years. Both groups were drawn on the basis of the selected examination of children from two Moscow districts. The criteria for risk factors involved the upper 5% of the distribution curve for blood pressure, the upper 10% of the distribution curve for cholesterol and triglycerides, the upper 15% of the distribution curve for the Quetelet index, and a positive response to the question on smoking, "Smoke at least once per week or more frequently?" METHODS: The intervention was carried out both among the entire sample population and more intensively among persons with risk factors. It included counseling for children and their parents on rational diet, physical activity, and smoking hazards. Relevant material on health education was disseminated. Follow-up examinations were carried out at 1 and 3 years following baseline measures. RESULTS: The examination at 1 year showed that the children of the intervention district had attained a greater reduction in their levels of total cholesterol, triglycerides, and systolic blood pressure than those of the reference district. High-density lipoprotein cholesterol levels decreased equally in both districts. After 3 years, the effect was retained for cholesterol and systolic blood pressure; the level of high-density lipoprotein cholesterol showed a greater reduction in district 2. After 1 year, the increase in the Quetelet index among the intervention sample (district 1) became less. After 3 years of intervention, the smoking accretion rate had decreased by 8.9% in district 1 (intervention) compared with that in district 2 (reference).

Blood Pressure↗

Tobacco smoking in Moscow school students.

A cross-sectional study on tobacco smoking prevalence and related socio-psychological parameters in Moscow school students aged 10-17 was performed. Data from an anonymous self-report (n = 4802) on smoking prevalence was confirmed by special technique--expert assessment. Widespread smoking was found: among male 5th graders (the youngest group) 14.4% are smokers (those who smoked at least 1 cigarette over the past 3 months); among male 10th graders (oldest group) 53.2% smoke; among females these figures were 0.8% for the youngest students and 28.2% for the oldest ones. A significant difference in awareness of smoking health hazards and attitudes towards the habit was shown among school students with various smoking statuses. Complaints about cough and shortness of breath after light physical stress were significantly more prevalent in regular smokers as compared to non-smokers. The possible causal role of some psychological factors in early formation of smoking habit is discussed.

Adolescent↗

Comparison of smoking prevalence in school students sampled from the United States of America and the Union of Soviet Socialist Republics.

To assess the smoking prevalence among adolescents in the USA and the USSR, students in Moscow and Minneapolis were surveyed by common protocol and identically trained staff. Smoking habits were measured by a self-report questionnaire and an expired air sample of carbon monoxide (CO). Significant gender differences were found between the two national groups. Among girls in the USA, there was a significantly higher rate of weekly smoking as compared to girls in the USSR. Among boys in the USSR as compared to those in the USA, there was a significantly higher rate of ever smokers and daily smokers, but also of ex-smokers. These gender differences may reflect cultural differences in smoking patterns between the two countries. Cigarette smoking is clearly a public health problem in both countries with its onset in adolescence.

Adolescent↗

The role of inhibitory processes in the formation of functional properties of neurons in vibrissal projection zone of the cat somatosensory cortex.

The role of intracortical inhibitory processes in the formation of neuronal receptive fields in the vibrissal projection zone of the somatosensory cortex was studied. Iontophoretic application of picrotoxin and bicuculline blocks the inhibition and causes the loss of directional sensitivity in neurons. Activation of inhibition by distant glutamate application gives opposite results--neurons become direction sensitive. A dependence was found between spatial location of activated cells and the pattern of changes of their detector properties. Inhibitory processes caused by natural afferent stimulation lead to similar changes in the functional properties of neurons.

Animals↗

Distribution of proteins in erythrocyte membranes from patients with hypertension.

The distribution of characteristic proteins in erythrocyte membranes was studied in patients with essential hypertension (EH) (n = 44), secondary hypertension of renal genesis (n = 42), and healthy persons (n = 44). Densitograms of gels analyzed after electrophoresis of erythrocyte ghosts showed a twofold increase in the amount of band 4.5 (Mw = 52-59 kD) and band 6 (Mw = 35 kD) polypeptides in EH patients as compared to that in healthy persons. Radioimmunoassay with monoclonal antibodies obtained to the sarcoplasmic reticulum (SR) of heart muscle has demonstrated that the amount of the antibodies bound to fragmented erythrocyte membranes from EH persons is greater by at least 28% than that in healthy people. Patients with secondary arterial hypertension of renal genesis did not reveal a significant difference in binding of monoclonal antibodies as compared to the control group. Thus, erythrocyte membranes from EH subjects are different from those taken from the blood of healthy people by the increased amount of bands 4.5 and 6 proteins.

Adult↗

Statistical analysis of nucleotide runs in coding and noncoding DNA sequences.

A statistical analysis of the occurrence of particular nucleotide runs in DNA sequences of different species has been carried out. There are considerable differences of run distributions in DNA sequences of procaryotes, invertebrates and vertebrates. There is an abundance of short runs (1-2 nucleotides long) in the coding sequences and there is a deficiency of such runs in the noncoding regions. However, some interesting exceptions from this rule exist for the run distribution of adenine in procaryotes and for the arrangement of purine-pyrimidine runs in eucaryotes. The similarity in the distributions of such runs in the coding and noncoding regions may be due to some structural features of the DNA molecule as a whole. Runs of guanine (or cytosine) of three to six nucleotides occur predominantly in noncoding DNA regions in eucaryotes, especially in vertebrates.

Animals↗

Computer analysis of R-looped DNA from electron micrographs.

The algorithms of the analysis of R-looped DNA molecules from electron micrographs are presented. We propose a two-dimensional R-loop distribution map with abscissa and ordinate axes corresponding to the positions of the left and right ends of the loop respectively. A transcription analysis of the hybrid plasmid pSCV1, which comprises heterologous genes from SV40 and pBR322, based on this map illustrates the program application.

DNA↗