Mechanical denaturation of globular protein in the solid state

A method for taking stress-strain diagrams in microsamples prepared from glutaraldehyde-treated monocrystals and amorphous films of hen egg-white lysozyme has been developed. Analysis of the diagrams has shown that the deformation obeys Hooke's law within 0-2%. Upon further deformation of a crystalline sample (up to 6-10%), when a critical stress, sigma(cr), is reached, the protein molecules in the sample denature and become greatly extended. Depending on the crystal type and crystallographic direction, the sample length increases 2-4 times. The critical stress is essentially dependent on the factors affecting intra- and intermolecular interactions: temperature, hydration level and urea concentration. Mechanisms for mechanical denaturation are proposed.     

Temperature dependence of the yield shear resultant and the plastic viscosity coefficient of erythrocyte membrane. Implications about molecular events during membrane failure.

Structural failure of the erythrocyte membrane in shear deformation occurs when the maximum shear resultant (force/length) exceeds a critical value, the yield shear resultant. When the yield shear resultant is exceeded, the membrane flows with a rate of deformation characterized by the plastic viscosity coefficient. The temperature dependence of the yield shear resultant and the plastic viscosity coefficient have been measured over the temperature range 10-40 degrees C. Over this range the yield shear resultant does not change significantly (+/- 15%), but the plastic viscosity coefficient changes exponentially from a value of 1.3 X 10(-2) surface poise (dyn s/cm) at 10 degrees C to a value of 6.2 X 10(-4) surface poise (SP) at 40 degrees C. The different temperature dependence of these two parameters is not surprising, inasmuch as they characterize different molecular events. The yield shear resultant depends on the number and strength of intermolecular connections within the membrane skeleton, whereas the plastic viscosity depends on the frictional interactions between molecular segments as they move past one another in the flowing surface. From the temperature dependence of the plastic viscosity, a temperature-viscosity coefficient, E, can be calculated: eta p = constant X exp(--E/RT). This quantity (E) is related to the probability that a molecular segment can "jump" to its next location in the flowing network. The temperature-viscosity coefficient for erythrocyte membrane above the elastic limit is calculated to be 18 kcal/mol, which is similar to coefficients for other polymeric materials.     

A simple cryogenic holder for tensile testing of soft biological tissues

To overcome the difficulty of gripping soft biological materials for tensile test, a simple inexpensive cryogenic holder was developed which allows rapid (3 min) preparation of samples. It is made of 6 parts, built in a bakelite cloth, which is an excellent thermal isolant, and is used with rectangular (8x10(-2)x10(-2)x10(-2)m) samples. The holder with the sample inside is completely immersed in liquid nitrogen for 50 s. This duration allows the freezing of the sample ends on a 10(-2)m length and gives a very flat freezing surface throughout the sample cross section. The 6x10(-2)m central part of the sample remained at ambient temperature. Two parts of the holder help maintain the sample until its ends are vertically gripped in the tensile machine thus avoiding any sample deformation during this step. No pressure was applied on the frozen part of the sample by grips of the tensile machine and this avoids breaks in this region. The sample is fixed by adhesion forces (>1 kN) between its frozen parts and 2 pieces of the holder. The procedure has been successfully tested with bovine and salmon muscle samples and results show tensile breaks randomly distributed in the unfrozen region of the samples. Particular attention has been paid to obtain a very flat freezing surface so that the axial strain is equal throughout the sample and therefore any strain-related mechanical parameters can be accurately determined. The dimensions of the holder can be easily modified to fit other sample geometries and can be used with other biological materials.     

A lyotrope gradient method for liquid crystal temperature-composition-mesomorph diagram construction using time-resolved x-ray diffraction.

A new method for rapidly constructing isobaric temperature-composition-mesomorph (T-C) diagrams is described. The method involves establishing a lyotrope concentration gradient in a liquid crystal lengthwise in an x-ray capillary tube. At a fixed temperature such a sample corresponds to an isotherm in the corresponding isobaric T-C diagram. The concentration gradient is conveniently established by bringing the two components into contact in the capillary and allowing limited diffusion of one component into the other. Phase boundaries are located and phases are identified and structurally characterized continuously along the length of the capillary using time-resolved x-ray diffraction. Repeating the measurement on the same sample at a series of temperatures in the range of interest completes that T-C diagram. The method has been used to construct the T-C diagram for detergent/water and lipid/water binary and ternary systems in the 20-120 degrees C range. They agree well with and extend the results obtained by conventional methods.     

Experimental study and analysis of mechanical properties of frozen rabbit aorta by fracture mechanics approach

In order to investigate fracture problems associated with cryopreservation of aorta, experiments were carried out to study the effects of temperature, freezing rate and cryoprotective agent on the fracture mechanics properties of frozen rabbit aorta and a test method for crack criterion of frozen rabbit aorta was developed. Results showed that as temperature decreases, the fracture modes of frozen rabbit aorta changed from typical ductile fracture to typical brittle fracture, the crack was more difficult to grow as temperature decreased, and its resist-fracture ability weakened remarkably from -20 to -80 degrees C. However, freezing rates had no effects on the fracture modes when sample was cooled to -50 degrees C, while the resist-fracture ability was stronger when the sample was cooled at a higher freezing rate. Due to the hydration action of dimethyl sulphoxide (DMSO), the rabbit aorta permeated by 10% (v/v) DMSO presented typical ductile fracture when it was cooled to -50 degrees C, so its resist-fracture ability was enhanced obviously. Compared to the axial sample, the circumferential sample's resist-fracture ability is better because of its larger deformation energy available.     

Excluded volume effect in unzipping DNA with a force

A double stranded DNA molecule when pulled with a force acting on one end of the molecule can become either partially or completely unzipped depending on the magnitude of the force F. For a random DNA sequence, the number M of unzipped base pairs goes as M approximately (F - Fc)(-2) and diverges at the critical force Fc with an exponent chi = 2. We find that when excluded volume effect is taken into account for the unzipped part of the DNA, the exponent chi = 2 is not changed but the critical force Fc is changed. The force versus temperature phase diagram depends on only two parameters in the model, the persistence length and the denaturation temperature. Furthermore a scaling form of the phase diagram can be found. This scaling form is parameter independent and depends only on the spatial dimension. It applies to all DNA molecules and should provide a useful framework for comparison with experiments.     

Telomere length measurement by fluorescence in situ hybridization and flow cytometry: tips and pitfalls

BACKGROUND: Telomeres containing noncoding DNA repeats at the end of the chromosomes are essential for chromosomal stability and are implicated in regulating the replication and senescence of cells. The gradual loss of telomere repeats in cells has been linked to aging and tumor development and methods to measure telomere length are of increasing interest. At least three methods for measuring the length of telomere repeats have been described: Southern blot analysis and quantitative fluorescence in situ hybridization using either digital fluorescence microscopy (Q-FISH) or flow cytometry (flow-FISH). Both Southern blot analysis and Q-FISH have specific limitations and are time-consuming, whereas the flow-FISH technique requires relatively few cells (10(5)) and can be completed in a single day. A further advantage of the flow-FISH method is that data on the telomere length from individual cells and subsets of cells (lymphocytes and granulocytes) can be acquired from the same sample. In order to obtain accurate and reproducible results using the flow-FISH technique, we systematically explored the influence of various steps in the protocol on telomere length values and established an acceptable range for the most critical parameters. METHODS: Isolated leukocytes from whole blood are denatured by heat and 70%/75% formamide, then hybridized with or without a telomere-specific fluorescein isothiocyante (FITC)-conjugated peptide nucleic acid probe (PNA). Unbound telomere PNA is washed away, the DNA is counterstained, and telomere fluorescence is measured on a flow cytometer using an argon ion laser (488 nm) to excite FITC. For each sample, duplicates of telomere PNA-stained and unstained tubes are analyzed. RESULTS: Cell counts and flow-FISH telomere length measurements were performed on leukocytes and thymocytes of humans and other species. Leukocyte suspensions were prepared by two red blood cell lysis steps with ammonium chloride. Optimal denaturation of DNA was achieved by heating at 85-87 degrees C for 15 min in a solution containing 70%/75% formamide. Hybridization was performed at room temperature with a 0.3 microg/ml telomere-PNA probe for at least 60-90 min. Unbound telomere-PNA probe was diluted at least 4,000-40,000 times with wash steps containing 70%/75% formamide at room temperature. LDS 751 and DAPI were suitable as DNA counterstains as they did not show significant interference with telomere length measurement. CONCLUSIONS: The use of flow-FISH for telomere length measurements in nucleated blood cells requires tight adherence to an optimized protocol. The method described here can be used to determine rapidly the telomere length in subsets of nucleated blood cells.     

Phase diagrams for DNA crystallization systems

Phase diagrams for several oligonucleotide duplex-spermine systems have been constructed. These diagrams characterize the duplex and spermine concentrations ranges in which crystalline precipitates are formed. All of them are wedge-like form. The slope of the upper branch of the diagram is determined by the oligonucleotide length. The position of the lower branch depends on both the nucleotide sequence and its length. The position of the lower branch depends on both the nucleotide sequence and its length. It has been shown that the addition to the system of MgCl2 and NaCl salts and MPD results in specific changes in the diagrams. A model for oligonucleotide duplex-spermine system has been suggested which explains the main characteristic features of the obtained phase diagrams. The experimental phase diagrams for the (pGpT)n (pApC)n-spermine system (n = 2,3,4) have been analyzed ion terms of this model and the values of the binding constants of spermine and Mg2+ ions binding to duplexes have been determined. It permitted to identify the complexes that precipitated in different regions of the phase diagrams under various conditions. The diagram obtained in the presence of a cobalt hexammine counterion is also considered. It has been shown that this phase diagram, in general, is similar to those obtained for the oligonucleotide duplex-spermine system.     

Modification of anomalous swelling in multilamellar vesicles induced by alkali halide salts

By use of small-angle X-ray scattering it is shown that addition of alkali halide salts in small amounts (0-200 mM) shifts the repeat spacing in multilamellar DC13PC vesicles and alters the anomalous swelling behaviour close to the main transition. Both effects follow the Hofmeister series of the ions. We suggest that the shift of repeat spacing can be explained by ion effects on the van der Waals attractive forces between the membranes and on the decay length of the repulsive hydration force. The anomalous swelling is explained in terms of a critical unbinding of the membranes. The proximity of the critical temperature of the unbinding to the main transition temperature can be tuned by varying the concentration and type of salt in the sample.     

Effects of lipid chain length and unsaturation on bicelles stability. A phosphorus NMR study

Most studies reported until now on the magnetically alignable system formed by the binary mixtures of long- and short-chain lipids were based on the mixture of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (D14PC) and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (D6PC) lipids. We have recently shown that a large part of the phase diagrams of this lipid mixture could be understood by taking into account the partial miscibility between the long-chain lipids and the short-chain lipids when the sample was heated above the melting transition temperature (Tm) of the long-chain lipids. In this work, we show by modifying the chain length of either one of the two lipids that it is possible to control their miscibility and thus the intervals of temperature and composition where spontaneous alignment is observed in a magnetic field. By using 31P NMR, we demonstrate that the very special properties of such binary lipid mixtures are correlated with the propensity for short-chain lipids to diffuse into the bilayer regions. We also show that lipid mixtures with comparable properties can be formed with unsaturated lipids such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC).     

Phase Diagrams for DNA Crystallization Systems

Abstract

Phase diagrams for several oligonucleotide duplex -spermine systems have been constructed. These diagrams characterize the duplex and spermine concentrations ranges in which crystalline precipitates are formed. All of them are wedge-like form. The slope of the upper branch of the diagram is determined by the oligonucleotide length. The position of the lower branch depends on both the nucleotide sequence and its length. The position of the lower branch depends on both the nucleotide sequence and its length. It has been shown that the addition to the system ofMgCl₂ and NaCl salts and MPD results in specific changes in the diagrams. A model for oligonucleotide duplex-spermine system has been suggested which explains the main characteristic features of the obtained phase diagrams. The experimental phase diagrams for the (pGpT)_n · (pApC)_n-spermine system (n = 2,3,4) have been analyzed ion terms of this model and the values of the binding constants of spermine and Mg²⁺ions binding to duplexes have been determined. It permitted to identify the complexes that precipitated in different regions of the phase diagrams under various conditions. The diagram obtained in the presence of a cobalt hexammine counterion is also considered. It has been shown that this phase diagram, in general, is similar to those obtained for the oligonucleotide duplex-spermine system.     

Bovine aorta actin. Development of an improved purification procedure and comparison of polymerization properties with actins from other types of muscle

Crude actin extracts from acetone-dried powder of the muscle layer of bovine aorta contain an actin-modulating protein which promotes nucleation of actin monomers and decreases the average length of actin filaments in a Ca2+-dependent manner. This observation has allowed the development of an improved purification procedure for aorta actin which increases the yield 2- to 3-times. The actin obtained with this procedure consists of 77% alpha- and 23% gamma-isoelectric species. Pure aorta actin is indistinguishable from actins from skeletal, cardiac and chicken-gizzard smooth muscle in its polymerization rate, critical concentration, and reduced viscosity when polymerized with KCl at 25 degrees C. It differs from sarcomeric actins, but not from chicken-gizzard smooth muscle actin, in the temperature dependence of polymerization equilibria in KCl. This difference correlates with the amino acid replacements Val-17----Cys-17 and Thr-89----Ser-89, supporting a conclusion drawn from other studies that the N-terminal portion of actin polypeptide chain contains sites important for polymerization.     

Seeing spots: complex phase behavior in simple membranes

Liquid domains in model lipid bilayers are frequently studied as models of raft domains in cell plasma membranes. Micron-scale liquid domains are easily produced in vesicles composed of ternary mixtures of a high melting temperature lipid, a low melting temperature lipid, and cholesterol. Here, we describe the rich phase behavior observed in binary and ternary systems. We then discuss experimental challenges inherent in mapping phase diagrams of even simple lipid systems. For example, miscibility behavior varies with lipid type, lipid ratio, lipid oxidation, and level of impurity. Liquid domains are often circular, but can become noncircular when membranes are near critical points. Finally, we reflect on applications of phase diagrams in model systems to rafts in cell membranes.     

Simulations of the erythrocyte cytoskeleton at large deformation. I. Microscopic models.

Three variations of a polymer chain model for the human erythrocyte cytoskeleton are used in large deformation simulations of microscopic membrane patches. Each model satisfies an experimental observation that the contour length of the spectrin tetramers making up the erythrocyte cytoskeleton is roughly square root of 7 times the end-to-end distance of the tetramer in vivo. Up to modest stress, each brushy cytoskeletal network behaves, consistently, like a low-temperature, planar network of Hookean springs, with a model-dependent effective spring constant, keff, in the range of 20-40 kBT/s(o)2, where T is the temperature and s(o) is the force-free spring length. However, several features observed at large deformation distinguish these models from spring networks: 1) Network dimensions do not expand without bound in approaching a critical isotropic tension (square root of 3 keff) that is a characteristic limit of Hookean spring nets. 2) In surface compression, steric interactions among the chain elements prevent a network collapse that is otherwise observed in compression of planar triangulated networks of springs. 3) Under uniaxial surface tension, isotropy of the network disappears only as the network is stretched by more than 50% of its equilibrium dimensions. Also found are definitively non-Hookean regimes in the stress dependence of the elastic moduli. Lastly, determinations of elastic moduli from both fluctuations and stress/strain relations prove to be consistent, implying that consistency should be expected among experimental determinations of these quantities.     

Analysis of welding Au nanowires into T junctions

The effects of temperature and size on the welding of Au nanowires (NWs) into T junctions is studied using molecular dynamics simulations based on the second-moment approximation of the many-body tight-binding potential. Simulation results show that when the top NW approaches the bottom one, it elongates towards the bottom one just before welding due to the interaction of the van der Waals attractive force. During welding, the bottom NW gradually reaches critical bend deformation through successive pressure applied from the top one, followed by buckling of the top NW. The structural order of NWs significantly decreases with increasing welding temperature or decreasing NW width. Welding at high temperatures (700 K or above) causes alignment difficulty due to an unstable NW geometry or even welding failure due to a decrease in NW length. Smaller NWs have larger stress during the welding process.     

Effect of Day and Night Temperature on Internode and Stem Length in Chrysanthemum: Is Everything Explained by DIF?

In many plant species, including chrysanthemum, a strong positive correlation between internode length and DIF [difference between day (DT) and night (NT) temperature] has been observed. However, Langton and Cockshull (1997. Scientia Horticulturae 69: 229-237) reported no such relationship and showed that absolute DT and NT explained internode length rather than DIF. To investigate these conflicting results and to clarify the validity of the DIF concept, cut chrysanthemums (Chrysanthemum 'Reagan Improved') were grown in growth chambers at all 16 combinations of four DT and four NT (16, 20, 24 and 28 degrees C) with a 12 h day length. Length of internode 10, number of internodes and stem length were measured on days 5, 10, 17, 22 and 27 after starting the temperature treatments. Internode length on day 10 showed a positive linear relationship with DIF (R2 = 0.64). However, when internodes had reached their final length in all treatments (day 27), a much stronger positive linear relation was observed (R2 = 0.81). A model to predict final internode length was developed based on the absolute DT and NT responses: both responses were optimum curves and no significant interaction between DT and NT occurred [final internode length (mm) = -32.23 + 3.56DT + 1.08NT - 0.0687DT2 - 0.0371NT2; R2 = 0.91, where TD is day temperature and TN is night temperature]. It is shown that DIF can predict final internode length only within a temperature range where effects of DT and NT are equal in magnitude and opposite in sign (18-24 degrees C). Internode appearance rate, as well as stem length formed during the experiment, showed an optimum response to DT.     

Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model

The transformation between a gel and a fluid phase in dipalmitoyl-phosphatidylcholine (DPPC) bilayers has been simulated using a coarse grained (CG) model by cooling bilayer patches composed of up to 8000 lipids. The critical step in the transformation process is the nucleation of a gel cluster consisting of 20-80 lipids, spanning both monolayers. After the formation of the critical cluster, a fast growth regime is entered. Growth slows when multiple gel domains start interacting, forming a percolating network. Long-lived fluid domains remain trapped and can be metastable on a microsecond time scale. From the temperature dependence of the rate of cluster growth, the line tension of the fluid-gel interface was estimated to be 3+/-2 pN. The reverse process is observed when heating the gel phase. No evidence is found for a hexatic phase as an intermediate stage of melting. The hysteresis observed in the freezing and melting transformation is found to depend both on the system size and on the time scale of the simulation. Extrapolating to macroscopic length and time scales, the transition temperature for heating and cooling converges to 295+/-5 K, in semi-quantitative agreement with the experimental value for DPPC (315 K). The phase transformation is associated with a drop in lateral mobility of the lipids by two orders of magnitude, and an increase in the rotational correlation time of the same order of magnitude. The lipid headgroups, however, remain fluid. These observations are in agreement with experimental findings, and show that the nature of the ordered phase obtained with the CG model is indeed a gel rather than a crystalline phase. Simulations performed at different levels of hydration furthermore show that the gel phase is stabilized at low hydration. A simulation of a small DPPC vesicle reveals that curvature has the opposite effect.     

Hydrostatic pressure induces hydrocarbon chain interdigitation in single-component phospholipid bilayers

By use of neutron diffraction for structural analysis, the temperature-pressure phase diagrams of several fully hydrated single-component phospholipid bilayers have been explored up to hydrostatic pressures of 2 kbars. The gel to liquid-crystalline phase transition temperature Tm increases linearly with pressure over a 10(-3)-2 kbar range in accordance with the Clausius-Clapeyron relationship giving dTm/dP values of 23.0 degrees C/kbar for 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) and 28.0 degrees C/kbar for 1,2-distearoyl-sn-glycero-3-phosphatidylcholine (DSPC). The so-called pretransition was not observed in the isothermal pressure experiments, suggesting that no appreciable volume change occurs at this transition. These results are in good agreement with those reported using other techniques. In addition, at pressures higher than the isothermal liquid-crystalline to gel transition pressure, a new pressure-induced phase transition was observed for DPPC and DSPC in which the hydrocarbon chains from apposing monolayers become interdigitated with the chains occupying a cross-sectional area approximately equal to 5% less than in the gel phase. The temperature-pressure phase diagrams show the gel-interdigitated phase boundaries to be highly curved and the minimum pressure at which interdigitation occurs to decrease with increasing hydrocarbon chain length.     

The opposite effect of temperature on polyethylene glycol-based aqueous biphasic systems versus aqueous biphasic extraction chromatographic resins

Variation in operational temperatures has revealed differences in the partitioning behavior of probe solutes between the phases in aqueous biphasic systems (ABS) and the related aqueous biphasic extraction chromatographic resin (ABEC). This difference has been studied using the hydrophobic anion, 99TcO4-, as a probe and (NH4)2SO4 as the kosmotropic salt. Distribution of the hydrophobic anion 99TcO4- to the PEG-rich phase in a MePEG-5000/(NH4)2SO4 ABS increases with increasing temperature, but decreases are observed in batch uptakes of this anion to ABEC resins from (NH4)2SO4 solutions. Phase diagrams were constructed at five different temperatures from 10 to 50 degreesC using cloud point titration for the ABS and a correlation between the phase divergence, measured in terms of tie line length (TLL), and the temperature of the partitioning system was verified. Thermodynamic parameters (deltaHdegrees,deltaSdegrees, deltaGdegrees, ) as a function of temperature were calculated for the various systems studied and the results imply thermodynamic differences between partitioning in ABS versus ABEC.