The diffusion-concentration product of oxygen in lipid bilayers using the spin-label T1 method

A method is described to measure the oxygen diffusion-concentration product, DO[O2], at any locus that can be probed or labeled using nitroxide radicals. The method is based on the dependence of the spin-lattice relaxation time T1 of the spin label on the bimolecular collision rate with oxygen. Strong Heisenberg exchange between spin label and oxygen contributes directly to T1 of the spin label, while dipolar interactions are negligible. Both time-domain and continuous wave saturation methods for studying T1 are considered. The method has been applied to phospholipid liposomes using fatty acid spin labels. A discontinuity in DO[O2] at the main phase transition was observed.     

Multiangular method for analysing molecular geometry from nuclear Overhauser effect results

A multiangular method, as an extension of a triangular method, has been developed in order to analyse the local conformation of a molecule in an atomic resolution from nuclear Overhauser effect results. When there is a rigid part in the molecule, and the nuclear Overhauser effect signals are observed between several spins attributed to the rigid part of the molecule and the target spin to be analysed, the geometrical probability density of the target spin can be found by the multiangulation method, using distances between spin pairs. The spin density is illustrated by a set of isograms similar to electron density maps from X-ray crystallographic analyses. The molecular model building is performed based upon the isograms. An application to the conformation analysis of transferred nuclear magnetic resonance results of NAD⁺, which binds to lactose dehydrogenace from Thermus caldophilus GK24, is described.     

Biophysics with nitroxyl radicals.

The present status of the spin labeling method as applied to Biophysics is examined. After an outline of the chemical and physical properties of NO radicals, the analysis of linear and non-linear ESR spectra of spin labels and the information it yields is described. The possibilities of the method are critically discussed in the light of recent experiments.     

Rapid assessment of liposomal stability in blood by an aqueous nitroxide spin label

An electron spin resonance method using an aqueous nitroxide spin label, 2,2,6,-tetramethyl-piperidine-N-oxyl-4-trimethyl-ammonium, for rapid assessment of liposome stability in blood is presented. The retention of the nitroxide in liposomes is measured by its electron spin resonance signal intensity, a procedure which does not require separation of the sample from the blood. Any nitroxide that is released from the liposomes is reduced by external ascorbic acid which is added to the sample. The method permits kinetic studies on the integrity of liposomes in the presence of destabilizing factors such as detergent, blood, or alteration in temperature.     

A kinetic method to establish the specificity of spin labelling of macromolecules.

A method has been devised for establishing the specificity of spin labelling of a macromolecule. Analysis of the rate of incorporation of spin label under different conditions permits the assignment of reacting groups to classes of differing reactivity. The method is illustrated for the enzyme glycogen phosphorylase b.     

Kinetic analysis-based quantitation of free radical generation in EPR spin trapping

Because short-lived reactive oxygen radicals such as superoxide have been implicated in a variety of disease processes, methods to measure their production quantitatively in biological systems are critical for understanding disease pathophysiology. Electron paramagnetic resonance (EPR) spin trapping is a direct and sensitive technique that has been used to study radical formation in biological systems. Short-lived oxygen free radicals react with the spin trap and produce paramagnetic adducts with much higher stability than that of the free radicals. In many cases, the quantity of the measured adduct is considered to be an adequate measure of the amount of the free radical generated. Although the intensity of the EPR signal reflects the magnitude of free radical generation, the actual quantity of radicals produced may be different due to modulation of the spin adduct kinetics caused by a variety of factors. Because the kinetics of spin trapping in biochemical and cellular systems is a complex process that is altered by the biochemical and cellular environment, it is not always possible to define all of the reactions that occur and the related kinetic parameters of the spin-trapping process. We present a method based on a combination of measured kinetic data for the formation and decay of the spin adduct alone with the parameters that control the kinetics of spin trapping and radical generation. The method is applied to quantitate superoxide trapping with 5-diethoxyphosphoryl-5-methyl-1-pyrroline N-oxide (DEPMPO). In principle, this method is broadly applicable to enable spin trapping-based quantitative determination of free radical generation in complex biological systems.     

Calculation of electron paramagnetic resonance spectra from Brownian dynamics trajectories: application to nitroxide side chains in proteins.

We present a method to simulate electron paramagnetic resonance spectra of spin-labeled proteins that explicitly includes the protein structure in the vicinity of the attached spin label. The method is applied to a spin-labeled polyleucine alpha-helix trimer. From short (6 ns) stochastic dynamics simulations of this trimer, an effective potential energy function is calculated. Interaction with secondary and tertiary structures determine the reorientational motion of the spin label side chains. After reduction to a single particle problem, long stochastic dynamic trajectories (700 ns) of the spin label side-chain reorientation are calculated from which the Lamor frequency trajectory and subsequently the electron paramagnetic resonance spectrum is determined. The simulated spectra agree well with experimental electron paramagnetic resonance spectra of bacteriorhodopsin mutants with spin labels in similar secondary and tertiary environments as in the polyleucine.     

Low microwave-amplitude ESR spectroscopy: measuring spin-relaxation interactions of moderately immobilized spin labels in proteins

Electron spin resonance (ESR) spectroscopy in combination with site-directed spin labeling (SDSL) is a powerful tool for determining protein structure, dynamics and interactions. We report here a method for determining interactions between spin labels and paramagnetic relaxation agents, which is performed under subsaturating conditions. The low microwave-field amplitude employed (h(1)<0.36 G) only requires standard, commercially available ESR equipment. The effect of relaxation enhancement on the spin-spin-relaxation time, T(2e), is measured by this method, and compared to classical progressive power saturation performed on a free spin label, (1-oxyl-2,2,5,5-tetramethyl-Delta(3)-pyrroline-3-methyl)methanethiosulfonate (MTSL), and a spin-labeled protein (Thermomyces lanuginosa lipase, TLL-I252C), employing the water-soluble relaxation agent chromium(III) oxalate (Crox) in concentrations between 0-10 mM. The low-amplitude theory showed excellent agreement with that of classical power saturation in quantifying Crox-induced relaxation enhancement. Low-amplitude measurements were then performed using a standard resonator, with Crox, on 11 spin-labeled TLL mutants displaying rotational correlation times in the motional narrowing regime. All spin-labeled proteins exhibited significant changes in T(2e). We postulate that this novel method is especially suitable for studying moderately immobilized spin labels, such as those positioned at exposed sites in a protein. This method should prove useful for research groups with access to any ESR instrumentation.     

"Distant spin trapping": a method for expanding the availability of spin trapping measurements

The technique of spin trapping is used to study a wide range of free radicals in various systems, including those generated in vitro and in vivo. But unfortunately, EPR spectrometers are not always immediately accessible at the site of experimentation, and therefore it is important to find a method that can preserve a radical adduct over longer periods of time. We describe here an alternative method in which the samples can be frozen and transported for EPR measurements at another site. Various spin adducts of DEPMPO were frozen and measured at 0 degrees C at various intervals after freezing to determine their stability in the frozen state. The radical adducts were generated by established methods and stored at two different temperatures; -196 degrees C (liquid nitrogen) and -80 degrees C (dry ice). The experiments were carried out in an aqueous solution with and without a model of reducing environment (2 mM ascorbate). The results indicate that it is feasible to store and transport spin adducts for subsequent analysis. We conclude that this approach, which we term "distant spin trapping", makes it feasible to transport samples to another site for EPR measurements. This should significantly expand the ability to use spin trapping in biology and medicine.     

Use of spin probe in the determination of oxygen consumption in human neutrophils

A quantitative method of the oxygen consumption rate measurement by human blood neutrophils upon their activation is described. This method is based on the spin exchange determination between 3-carbamoyl-2,2,5,5-tetramethyl-3-pyrroline-1-yloxyl spin probe and oxygen molecules from the ESR spectra. Method allows the determination of about 1 micromolar concentrations of oxygen.     

Exploring protein conformations in vitro and in cell with EPR distance measurements

The electron–electron double resonance (DEER) method, which provides distance distributions between two spin labels, attached site specifically to biomolecules (proteins and nucleic acids), is currently a well-recognized biophysical tool in structural biology. The most commonly used spin labels are based on nitroxide stable radicals, conjugated to the proteins primarily via native or engineered cysteine residues. However, in recent years, new spin labels, along with different labeling chemistries, have been introduced, driven in part by the desire to study structural and dynamical properties of biomolecules in their native environment, the cell. This mini-review focuses on these new spin labels, which allow for DEER on orthogonal spin labels, and on the state of the art methods for in-cell DEER distance measurements.     

Spin diffusion in globular proteins: alpha-lactalbumin

The structural properties of globular proteins analyzed by two different methods: high-resolution NMR and circular dichroism were compared. We established that the spin diffusion method shows changes in the secondary structure during the unfolding of the alpha-lactalbumin molten globule by urea. It was shown that the spin diffusion method is extremely effective in studies of interactions of water and denaturant molecules with the protein both in the native and the molten globule states.     

ESR studies on the active intermediate in the enzymatic reduction of the Fe-bleomycin complex

The spin trapping method was applied to elucidate the active intermediate during the enzymatic reduction of Fe(III)-bleomycin in the presence of NADPH-cytochrome P-450 reductase and O2. Although the hydroxyl adducts to spin traps were observed, the adduct formation was not inhibited by catalase nor by SOD. Furthermore, in Tris-HCl buffer, no Tris adduct to the spin trap was observed. The results lead to the conclusion that there is no participation of free OH radical in the reactive intermediate in this reduction system. Effect of phosphate buffer on the reactivity of Fe(II)-bleomycin and spin state of Fe(III)-bleomycin were discussed.     

Technical note: Efficiency of total demineralization and ion‐exchange column for DNA extraction from bone

We investigated whether a combination of recently introduced methods, total demineralization and ion‐exchange columns, would increase DNA recovery from old bone. Ten bone samples taken after a burial period of ∼60 years were used in this study. Bone powder was digested using total or incomplete demineralization. DNA was extracted by the standard organic method. The DNA extract was purified with ion‐exchange columns or QIAquick® spin columns. The efficiency of different DNA extraction methods was compared in terms of DNA concentration, inhibitors generated by real‐time PCR, and conventional STR typing results. The mean DNA concentration using the total demineralization method is ∼3 times higher than that using the incomplete demineralization method. For DNA purification, the method using QIAquick® spin columns appeared to yield approximately double the DNA than the method using ion‐exchange columns. Furthermore, 2 out of 10 samples showed higher levels of inhibition with C_T values of IPC ≥30 cycles when using only ion‐exchange columns. In STR results, total demineralization yielded more locus profiles by 4.2 loci than incomplete demineralization, and QIAquick® spin columns also yielded more locus profiles by 3.5 loci than ion‐exchange columns. Total demineralization of bone powder significantly increased DNA yield and improved STR typing results. However, the use of ion‐exchange columns was not efficient when compared with the method using QIAquick® spin columns. It is suggested that the combination of total demineralization and QIAquick® spin columns lead to greatly improved STR typing results. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

A transient spin-state change during alkaline isomerization of ferricytochrome c

Kinetic difference spectra during the alkaline isomerization of ferricytochrome c were obtained by the pH-jump method in the range of 540 to 655 nm. The spectrum of the transient intermediate, which appears during the course of the isomerization, was reproduced from the spectra. The intermediate showed an intense absorption band at 600 nm, indicating that it is a high spin or mixed spin species. This is in contrast to the stable neutral and alkaline forms which are low spin species. The transient spin-state change during the isomerization was also observed upon rapid oxidation of ferrocytochrome c at alkaline pH.     

Modulating effect of new potential antimelanomic agents, spin-labeled triazenes and nitrosoureas on the DOPA-oxidase activity of tyrosinase

The modulating effect of newly synthesized alkylating spin labeled triazene and spin labeled nitrosourea derivatives on the DOPA-oxidase activity of mushroom tyrosinase has been investigated by Bumett's spectrophotometric method (Burnett et al., 1967). All spin labeled triazenes have exhibited activating effect on DOPA-oxidase activity of tyrosinase, whereas clinically used triazene (DTIC), which does not contain nitroxide moiety, have showed inhibiting effect. At the same experimental conditions the spin labeled aminoacid nitrosoureas have showed dual effect - activating, in the beginning of the enzyme reaction and inhibiting later on. It is deduced that the activating effect of the spin labeled compounds is due to the nitroxide moiety and the inhibiting effect of all compounds depends on their half-life time. This study might contribute to make more clear the mechanism of action of the new compounds and on the other hand would come in quite useful as a preliminary prognosis for their antimelanomic activity.     

The Role of the Fast Motion of the Spin Label in the Interpretation of EPR Spectra for Spin-Labeled Macromolecules

Abstract

The spin label method was used to observe the nature of the fast motions of side chains in protein monocrystals. The EPR spectra of spin-labeled lysozyme monocrystals (with different orientations of the tetragonal protein crystal in relation to the direction of the magnetic field) were interpreted using the method of molecular dynamics (MD). Within the proposed simple model, MD calculations of the spin label motion trajectories are performed in a reasonable real time. The model regards the protein molecule as frozen as a whole and the spin labeled amino acid residue as unfrozen. To calculate the trajectories in vacuum, a model of spin-labeled lysozyme was assembled, and the parameters of the force fields were specified for atoms of the protein molecule, including the spin label. The calculations show that the protein environment sterically limits the area of the possible angular reorientations for the NO reporter group of the nitroxide (within the spin label), and this, in turn, affects the shape of the EPR spectrum. However, it turned out that the spread in the positions of the reporter group in the angle space strictly adheres to the Gaussian distribution. Using the coordinates of the spin label atoms obtained by the MD method within a selected time range and considering the distribution of the spin label states over the ensemble of spin-labeled macro- molecules in a crystal, the EPR spectra of spin-labeled lysozyme monocrystals were simulated. The resultant theoretical EPR spectra appeared to be similar to experimental ones.     

Role of rapid movement of spin labels in interpreting EPR spectra for spin-labelled macromolecules

The method of spin labeling was used to monitor quick movements of side residues in protein monocrystals. The EPR spectra of monocrystals of spin-labeled lysozyme at different orientations of the tetrahonal crystal relative to the direction of the magnetic field were interpreted using the molecular dynamics method. A simple model was proposed, which enables one to calculate the trajectory of movements of the spin label by the molecular dynamic method over a relatively short period of time. The entire "frozen" protein molecule and a "defrozen" spin-labeled amino acid residue were considered in the framework of the model. To calculate the trajectories in vacuum, a model of spin-labeled lysozyme was constructed, and the parameters of force potentials for the atoms of the protein molecule and the spin label were specified. It follows from the calculations that the protein environment sterically hinders the range of eventual angular reorientations of the reporter NO-group of nitroxyl incorporated into the spin label, thereby affecting the shape of the EPR spectrum. However, the scatter in the positions of the reporter group in the angular space turned out to correspond to the Gauss distribution. Using the atomic coordinates of the spin label, obtained in a chosen time interval by the method of molecular dynamics, and taking into account the distribution of the states of the spin label in the ensemble of spin-labeled macromolecules in the crystal, we simulated the EPR spectra of monocrystals of spin-labeled lysozyme. The theoretical EPR spectra coincide well with the experimental.     

Binding and incorporation of lecithin-cholesterol vesicles to lymphocytes: A spin-label study

Summary When lecithin-cholesterol vesicles, containing the membrane-bound spin probe 3-doxyl-cholestane, were set in contact with mouse lymphocytes, the vesicles adsorbed to the cell and vesicle-membrane components were transferred to it. The spin probe was enzymatically reduced at the inside of the cell membrane. The spin-label method provided a means to determine quantitatively the extent of vesicles adsorption and vesicle-cell fusion by measuring the transfer of vesicles membrane material to the cell. This method, together with the reduction of spin label by the cell, allowed also a quantitative estimate of the extent of endocytosis during cell-liposome interaction.     

Transverse motion of chlorophyll derivatives in phospholipid bilayers

Chlorophyll derivatives were synthesized with spin labels attached to the porphyrin ring. These labels were incorporated into egg phosphatidylcholine vesicles in order to estimate the transbilayer motion (flip-flop) of this class of photosynthetic pigments. Using the ascorbate reduction method, the upper limit to the spin label half-life is tau 1/2 approximately 4 min at 0 degrees C. The flip-flop rate is rapid compared to that of a phospholipid spin label under the same conditions. The presence or absence of magnesium in the center of the porphyrin ring had no measurable effect on the flip-flop rate.