Biomedical subjects

D P Kharakoz

Publications and source records attributed to D P Kharakoz.

13 recordsLinked to original sources

PubMed2004

Structure and fluctuations of phosphatidylcholines in the vicinity of the main phase transition.

We have determined the structural properties and bending fluctuations of fully hydrated phosphatidylcholine multibilayers in the fluid (Lalpha) phase, as well as the structure of the ripple (Pbeta') phase near the main phase transition temperature (TM) by x-ray diffraction. The number of carbons, nHC, per acyl chain of the studied disaturated lipids varied from 14 to 22. All lipids exhibit a nonlinear increase of the lamellar repeat distance d in the Lalpha phase upon approaching TM, known as "anomalous swelling." The nonlinear increase reduces with chain length, but levels off at a constant value of about 0.5 A for lipids with more than 18 hydrocarbons per chain. A detailed analysis shows that anomalous swelling has two components. One is due to an expansion of the water layer, which decreases with chain length and finally vanishes for nHC >18. The second component is due to a bilayer thickness increase, which remains unchanged in its temperature dependence, including a nonlinear component of about 0.5 A in the vicinity of TM. Thus, anomalous swelling above 18 hydrocarbons per chain is due to the pretransitional effects on the membrane only. These results are supported by a bending fluctuation analysis revealing increased undulations close to TM only for the short chain lipids. We have further calculated the electron density maps in the ripple phase and find no coupling of the magnitude of the ripple amplitude to the chain length effects observed in the Lalpha phase. Hence, in agreement with an earlier report by Mason et al. [Phys. Rev. E 63, 030902 (2001)] there is no connection between the formation of the ripple phase and anomalous swelling.

Biophysics↗

PubMed2001

Phase-transition-driven synaptic exocytosis: a hypothesis and its physiological and evolutionary implications.

It is proposed that the plasma membrane in the active zones of synaptic terminals contains self-assembling cooperative domains whose Ca2+-induced solidification may be the driving force of the fast neurotransmitter release in the central synapses. This hypothesis and a qualitative model of the phase-transition-driven exocytosis provide formulation of a unitary approach to a number of general problems in the physiology of animals. It allows answering the following questions, among others: (i) What is the physical reason for the existence of a narrow optimum range of body temperatures in warm-blooded species? (ii) What is the physical reason for the inevitable necessity of regular sleep in animals? (iii) Does there indeed exist any general mechanism of general anesthesia?

Anesthetics, General↗

PubMed2000

Protein compressibility, dynamics, and pressure.

The relationship between the elastic and dynamic properties of native globular proteins is considered on the basis of a wide set of reported experimental data. The formation of a small cavity, capable of accommodating water, in the protein interior is associated with the elastic deformation, whose contribution to the free energy considerably exceeds the heat motion energy. Mechanically, the protein molecule is a highly nonlinear system. This means that its compressibility sharply decreases upon compression. The mechanical nonlinearity results in the following consequences related to the intramolecular dynamics of proteins: 1) The sign of the electrostriction effect in the protein matrix is opposite that observed in liquids-this is an additional indication that protein behaves like a solid particle. 2) The diffusion of an ion from the solvent to the interior of a protein should depend on pressure nonmonotonically: at low pressure diffusion is suppressed, while at high pressure it is enhanced. Such behavior is expected to display itself in any dynamic process depending on ion diffusion. Qualitative and quantitative expectations ensuing from the mechanical properties are concordant with the available experimental data on hydrogen exchange in native proteins at ambient and high pressure.

Compressive Strength↗

PubMed1999

Stoichiometry of dipalmitoylphosphatidylcholine-DNA interaction in the presence of Ca2+: a temperature-scanning ultrasonic study.

DNA-DPPC complexes can be prepared by means of a single step procedure of mixing DNA solution and aqueous lipid dispersion in the presence of calcium ions. Interaction between DPPC and DNA brings about a biphasic shape of melting curves corresponding to the free lipid and the strongly bound one. The amount of the strongly bound lipid is 5 molecules per nucleotide which is close to the size of the first lipid monolayer around DNA molecule.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1997

Partial volumes and compressibilities of extended polypeptide chains in aqueous solution: additivity scheme and implication of protein unfolding at normal and high pressure.

An empirical additivity method for calculation of the partial volumes and adiabatic compressibilities of extended oligo- and polypeptides having arbitrary amino acid compositions has been developed and tested by comparison with available experimental data. Its accuracy is the best among the known empirical approaches. Comparison of experimental data on protein denaturation with the results of calculation allows one to discriminate between the unfolded and molten globule states of globular proteins and to estimate the extent of unfolding. For the first time, experimental nonlinear data for the volume-pressure relationship in proteins and model compounds have been used to interpret the high-pressure denaturation of proteins. It has been shown that the two denatured states, molten globule and unfolded ones, can be attained by a pressure rise: the molten globule state by moderate pressure and the unfolded one by high pressure. The relationship between volumetric properties and hydration is briefly discussed.

Peptides↗

PubMed1997

Molten globule of human alpha-lactalbumin: hydration, density, and compressibility of the interior.

Specific partial volume, partial compressibility, and sound absorption changes induced by the native-to-molten globule state (acid) transition of the human alpha-lactalbumin were measured by means of densitometric and ultrasonic techniques and interpreted in terms of the protein molecule phase transition and interphase water transfer. The molten globule is a highly hydrated state containing about 270 water molecules inside. Intrinsic mass density of the hydrated (swollen) interior of the protein molecule is 5% smaller and the intrinsic compressibility coefficient 2 times higher than those in the native molecule. The obtained intrinsic compressibility falls into the range of values characteristic of highly associated liquids. Water inside the molten globule interior occupies less volume and is less compressible than in solvent phase. The acoustic relaxation was found to increase indicating an appearance of pressure-dependent processes. The commonly used approach to the calculation of the volume fluctuations of protein molecules, based on the well-known relation between the volume fluctuations and compressibility, is of limited applicability to the highly hydrated molten globule state because a large, if not predominant, part of the fluctuations may be determined by the process of water exchange between the molten globule and bulk solvent.

Densitometry↗

PubMed1993

Hydrational and intrinsic compressibilities of globular proteins.

Partial compressibilities of globular proteins in water are reviewed. Contribution of hydrational and of intrinsic compressibilities to experimental partial quantity have been evaluated from ultrasonic data using two independent methods: (a) additive calculation of the hydrational contributions of the surface atomic groups and (b) an analysis of correlation between partial compressibility and molecular surface area. The value (14 +/- 3) X 10(-6) bar(-1) for the isothermal compressibility coefficient of the protein interior at 25 degrees C was obtained as an average value for variety of globular proteins. This value is similar to that of solid organic polymers. Possible relaxation contribution to partial compressibility is roughly estimated from comparison of thermodynamic with x-ray data on protein compressibility. The average compressibility of water in the hydration shell of proteins was found to be 35 X 10(-6) bar(-1), which is 20% less than that of pure water.

Animals↗

PubMed1993

Ultrasonic study of melittin effects on phospholipid model membranes.

Low dose effects of melittin on dilute suspensions of dipalmitoylphosphatidylcholine multilamellar vesicles are investigated by studying the acoustic properties of the system. The temperature dependencies of sound velocity and absorption have been measured at 7.2 MHz in the temperature range of 20-55 degrees C, for different peptide/lipid molar ratios, R. The most pronounced effects were observed at R = 5 x 10(-3), in the vicinity of the pretransition, with a simultaneous increase in sound absorption and velocity. This indicates that melittin affects the polar head group region of the bilayer resulting in a decrease in mobility of the polar head groups. A nonmonotonic dependence of the main transition temperature, with an initial decrease followed by an increase as melittin is added, is interpreted as a consequence of a destabilizing action of the interfaces between mellitin-affected clusters and the unaffected phase.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1991

Coupling of sequential transitions in a DNA double hairpin: energetics, ion binding, and hydration.

In an effort to evaluate the relative contributions of sequence, ion binding, and hydration to the thermodynamic stability of nucleic acids, we have investigated the melting behavior of a double hairpin and that of its component single hairpins. Temperature-dependent UV absorption and differential scanning calorimetry techniques have been used to characterize the helix-coil transitions of three deoxyoligonucleotides: d(GTACT5GTAC), d(GCGCT5GCGC), and d(GCGCT5GCGCGTACT5GTAC). The first two oligomers melt with transition temperatures equal to 28 and 69 degrees C, respectively, in 10 mM dibasic sodium phosphate at pH 7.0. The Tm's are independent of strand concentration, strongly indicating the presence of single-stranded hairpin structures at low temperatures. The third oligomer, with a sequence corresponding to the joined sequences of the first two oligomers, melts with two apparently independent monomolecular transitions with Tm's of 41 and 69 degrees C. These transitions correspond to the melting of a double hairpin. In the salt range of 10-100 mM in NaCl, we obtain average enthalpies of 24 and 38 kcal/mol for the transitions in the single-hairpin molecules. Each transition in the double hairpin has an enthalpy of 32 kcal/mol. In addition, dtm/d log [Na+] for the transitions are 4.1 and 4.7 degrees C for the single hairpins and 12.6 and 11.2 degrees C for each transition in the double hairpin. The differential ion binding parameter between the double hairpin and that of the sum of single hairpins is roughly equal to 1.1 mol of Na+ ions/mol of double hairpin and is consistent with an increase in the electrostatic behavior of the stem phosphates of this molecule.

Base Composition↗

PubMed1989

Volumetric properties of proteins and their analogs in diluted water solutions. 1. Partial volumes of amino acids at 15-55 degrees C.

The apparent volumes of 14 amino acids in aqueous solutions at a concentration of 3 mg/ml were measured densitometrically within the temperature range 15-55 degrees C. The accuracy of measurements was +/- 0.3%. The decrease in volume of polar and charged atomic groups as well as the temperature dependences of the partial volumes was analysed. The differences in behaviour between charged, polar and nonpolar atomic groups were considered.

Amino Acids↗

PubMedDate not supplied

[Phase transition in lipids and the problem of homoiothermia].

Why such a high stability of temperature is necessary for warm-blooded animals? Why the range of body temperatures of various warm-blooded species is several-fold narrower than the range of environmental temperatures? What were the physicochemical factors that determined such results of the biological evolution? A hypothesis presented in this short communication provides answers to these basic questions of the problem of homoiothermia. The hypothesis implies that the Ca(2+)-induced chain-ordering phase transition in the lipid component of synaptic membranes plays a key role at the last step of the mechanism of synaptic transmission, namely, the step of neurotransmitter release. The physicochemical substantiation of a possible molecular mechanism of the release involving the phase transition is presented, and the main kinetic and evolutionary issues of the mechanism are considered in brief.

Animals↗

PubMedDate not supplied

[Nonlinear elasticity and dynamics of globular proteins].

A molecule of native protein exhibits a high degree of mechanical nonlinearity, which gives rise to a peculiar dynamics behavior of globular proteins. Intramolecular motions strongly depend on pressure. The reaction of specific volume to the action of electric field (electrostriction) inside the molecule has a sign opposite to that observed in liquids. The probability that a small ion would penetrate inside the globule from the solvent depends nonmonotonously on hydrostatic pressure. The nonmonotonicity should manifest itself in all processes related to the transfer of ions inside the globule. The relationship between the mechanical properties of the protein and the kinetics of hydrogen exchange at normal and high pressure is discussed.

Elasticity↗

PubMedDate not supplied

[Changes in the contractibility of the cytochrome c globule during redox transition].

Changes of the volume and compressibility of cytochrome c molecule in solution during red-ox transition were investigated using differential measurements of density and ultrasound velocity. Small changes were obtained: intrinsic compressibility of the globule increases by (2.5 +/- 1)% and intrinsic volume increases by not more than 0.2%. The results are in contradiction with the recently reported data of Eden et al. claiming that oxidation of the protein is accompanied by a large, of about 40%, increase of compressibility. The validity of our results is verified by three different methods; by comparison of independently measured absolute values of apparent volumes and compressibilities of the oxidized and reduced protein (i); by differential densimetric and ultrasound velocimetric titrations of oxidized cytochrome with ascorbate (ii) and of reduced cytochrome with ferricyanide (iii). The obtained data lead to the conclusion that oxidation-induced-changes of the root mean square amplitude for intramolecular motion of atoms of cytochrome c globule is really 50-fold less than that estimated from X-ray data.

Animals↗