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PubMed1990

Base dynamics of local Z-DNA conformations as detected by electron paramagnetic resonance with spin-labeled deoxycytidine analogues.

Conformation detection and base dynamics of spin-labeled Z-DNA have been investigated by electron paramagnetic resonance (EPR) spectroscopy. The two synthesized and characterized probes used in this study were C(5)-nitroxide-labeled 2'-deoxycytidine 5'-triphosphates, pppDCAT and pppDCAVAT, which serve as suitable substrates for Micrococcus luteus DNA polymerase. Enzymatic incorporation of these probes into (dG-dC)n yields the EPR-active alternating copolymers (dG-dC,DCAT)n and (dG-dC,-DCAVAT)n. These polymers assume typical B- and Z-DNA conformations under respective low (0.1 M NaCl) and high (4.5 M NaCl) salt conditions, as evidenced by their UV-circular dichroism spectra. The EPR line shape of (dG-dC,DCAT)n in Z-form is unique and significantly different from the B-form EPR spectrum. A similar observation is made for (dG-dC,DCAVAT)n. Thus, the EPR line shapes of these spin-labeled DNAs are indicative of their local conformations. The EPR spectra, analyzed with a previously published motional model [Kao, S.-C., Polnaszek, C.F., Toppin, C.R., & Bobst, A.M. (1983) Biochemistry 22, 5563-5568], indicate tau perpendicular values of 4 and 7 ns for the B- and Z-forms, respectively. Therefore, the base dynamics of Z-DNA are about two times slower than in B-DNA.

Circular Dichroism↗
PubMed2001

Stratum corneum protein dynamics as evaluated by a spin-label maleimide derivative: effect of urea.

The stratum corneum (SC) protein dynamics in the sulfhydryl group regions was studied by electron paramagnetic resonance (EPR) spectroscopy of a covalently attached maleimide derivative spin label. A two-state model for the nitroxide described the coexistence of two spectral components in the EPR spectra. The so-called strongly immobilized component arises from a spin-label fraction with the nitroxide moiety hydrogen-bonded to protein (rigid structure) and the weakly immobilized component is provided by the spin labels with higher mobility (approximately 10 times greater) exposed to the aqueous environment. The relative populations between these two states are in thermodynamic equilibrium. The apparent energetic gain for the nitroxide to form a hydrogen bond with the backbone rather than to be dissolved in the local environment was approximately 10 kcal/mol in the temperature range of 2-30 degrees C and approximately 6 kcal/mol in the range of 30-70 degrees C. Urea treatment caused a drastic increase in the segmental motion of the polypeptide chains that was completely reversible by its removal. Our analyses also indicated that the urea induced unfolding of the SC proteins opening the thiol group cavities. This work can also be useful to improve the spectral analysis of site-directed spin-labeling, especially for a more quantitative description of the nitroxide side chain mobility.

Albumins↗
PubMed1995

Spin-labeling study of the oxidative damage to low-density lipoprotein.

In this study, we have spin-labeled the lysine and cysteine residues of low-density lipoprotein (LDL) using N-4-(2,2,6,6-tetramethylpiperidinyl-1-oxyl-4-yl) maleimide (MAL-6) and succinimidyl-2,2,5,5-tetramethyl-3-pyrroline-1-oxyl-3-carboxylate (SSL), respectively. The electron spin resonance (ESR) spectrum of SSL bound to LDL indicated that the nitroxide moiety was relatively mobile. In contrast, the ESR spectrum of MAL-6 bound to LDL showed that the nitroxide moiety was rotationally restricted. Using the continuous-wave power saturation technique in the presence of hydrophobic and hydrophilic paramagnetic relaxing agents, we have determined that (i) approximately 60-70% of lysine-bound SSL is exposed to the aqueous phase, (ii) approximately 30-40% of SSL-LDL is buried in a hydrophobic region, and (iii) MAL-6 bound to LDL is localized predominantly in the hydrophobic region. During Cu(2+)-initiated oxidation of spin-labeled LDL, nitroxide labels located in a hydrophobic environment were predominantly degraded. Nitroxide destruction was inhibited by butylated hydroxytoluene, indicating the role of lipid peroxidation in this process. ESR data also showed that Cu2+ binding to lysine is essential for LDL oxidation. The spin label methodology may be useful for the investigation of site-specific radical reactions in LDL.

Apolipoproteins B↗
PubMed1985

Equilibrium of conformers in solution: spin-labelled angiotensin.

The number of structural parameters were determined for spin-labelled angiotensin in aqueous solution with the use of fluorescence spectroscopy and 1H NMR relaxation induced by the spin label. At the same time all measured parameters were estimated theoretically by means of energy calculations and Monte-Carlo techniques. The matching procedure for experimental and computational data allows one to suggest a dynamic equilibrium between conformers of the molecule in aqueous solution and to estimate the values of their weights.

Angiotensin II↗
PubMed1970

Electron paramagnetic resonance studies of spin-labeled hemoglobins and their implications to the nature of cooperative oxygen binding to hemoglobin.

The spin label technique has been used to study human hemoglobins A, F, Zürich, and Chesapeake as a function of carbon monoxide saturation. The experimental results suggest that the changes in the electron paramagnetic resonance spectra of hemoglobin labeled with N-(1-oxyl-2,2,6,6-tetramethyl-4-piperidinyl)iodoacetamide depend on the state of ligation of more than one heme group. For those hemoglobins with full or large cooperative ligand binding (such as A, F, and Zürich), there is a lack of isosbestic points in the spectra as a function of CO saturation. However, for those hemoglobins with little or no cooperative ligand binding (such as Chesapeake and methemoglobins), there is a sharp set of isosbestic points. These findings confirm and extend the early work of McConnell and co-workers. The absence of a set of isosbestic points in those hemoglobins with full cooperative ligand binding is consistent with the sequential model of Koshland, Némethy, and Filmer for cooperative oxygen binding to hemoglobin. The present results, with hemoglobin variants having known amino acid substitutions, also focus on the importance of the interactions among the amino acid residues located at alpha(1)-beta(2) or alpha(2)-beta(1) subunit contacts for the functioning of hemoglobin as an oxygen carrier. In addition, the resonance spectra of the spin label are very sensitive to small structural variations around the heme groups in the beta- or gamma-chains where the labels are attached. The results of the spin label experiment are discussed in relation to recent findings on the mechanism of oxygenation of hemoglobin from the nuclear magnetic resonance studies of this laboratory and the x-ray crystallographic analysis of Perutz and co-workers.

Amides↗
PubMed1978

Quantitative studies on competitive ligand binding to bovine serum albumin by use of the spin label 5-doxyl dodecanoic acid.

The binding of the spin label 5-doxyl dodecanoic acid to bovine serum albumin in phosphate buffer at pH 7.4 was studied by electron spin resonance spectroscopy. Free label and label bound to serum albumin could be quantitatively measured and evaluated from the superposition spectra of these two species with no previous separation. The efficiency relative to the spin label as competitors for binding to serum albumin was studied with salicylic acid and some fatty acids of medium length. The results were represented both by the stoichiometric model involving equilibrium constants Ki, by binding isotherms constructed from the Ki values, and by a purely graphical representation of the experimental data points without connection with any special binding model.

Binding, Competitive↗
PubMed1993

Extension of the parallax analysis of membrane penetration depth to the polar region of model membranes: use of fluorescence quenching by a spin-label attached to the phospholipid polar headgroup.

The parallax method is a method by which the depth of fluorescent molecules within a membrane is calculated from the ratio of quenching induced by two spin-labeled phospholipids at different depths. In this report, the method is extended to measurements of depth in the polar headgroup region of the membrane through use of a lipid with a spin-label attached to the polar choline moiety. Quenching data indicate that the choline-attached nitroxide is close to 19.5 A from the bilayer center, in good agreement with the choline location previously determined by diffraction measurements. By using quenching results obtained with this polar headgroup-labeled phospholipid, depths more accurate than those measured previously can be obtained for fluorophores in the polar region of the membrane. It appears that the most reliable results are obtained when depth is calculated from the quenching of the two spin-labels that quench a specific fluorophore most strongly. Applying this approach to a series of anthroyloxy-labeled fatty acids indicates that the depth of the anthroyloxy group is almost linearly related to the number of carbon atoms between it and the carboxyl group. The fatty acid carboxyl group itself is close to 18.6 A from the bilayer center in the ionized form and 16 A from bilayer center in the protonated form. This is close to the depth of the carboxyl groups on phospholipid fatty acyl chains. More accurate depths have also been obtained for 7-nitro-2,1,3-benzoxadiazol-4-yl (NBD) labeled phospholipids using the quenching of the choline-attached spin-label.(ABSTRACT TRUNCATED AT 250 WORDS)

4-Chloro-7-nitrobenzofurazan↗
PubMed2001

Effect of lung inflation on arterial spin labeling signal in MR perfusion imaging of human lung.

The effect of lung inflation on arterial spin-labeling signal in lung perfusion is investigated. Arterial spin-labeling schemes, called alternation of selective inversion pulse (ASI) and its hybrid (HASI), which uses blood water as an endogenous, freely diffusible tracer, were applied to magnetic resonance (MR) perfusion imaging of the lung. Perfusion-weighted images of the lung from nine healthy volunteers were obtained at different time delays. There was a significant signal difference in ASI images acquired at different respiratory phases. Greater signal enhancement has been observed when the volunteers performed breath holding on end expiration than on end inspiration. This is in agreement with the normal physiologic effect of lung inflation on the pressure-flow relationship of pulmonary vasculature. ASI and HASI perfusion-weighted images show similar lung features and image quality. Preliminary results from pulmonary embolism patients indicate that arterial spin labeling is sensitive for the detection of areas of perfusion deficit. J. Magn. Reson. Imaging 2001;13:954-959.

Adult↗
PubMed2005

Dynamics and partitioning of spin-labeled stearates into the lipid domain of stratum corneum.

The EPR spectra of the positional isomers n-doxyl stearic acids (n-DSA), with n=5, 12 and 16, and 5-doxyl methyl stearate (5-DMS) structured in the lipid domain of intact stratum corneum (SC), are characterized by the thermodynamic equilibrium of two distinct spectral components provided by two different motional states of the spin-labeled chains. A two-component model used in the EPR spectra simulations provided the relative populations of the components, allowing for the calculation of the thermodynamic profile. Based on a detailed investigation, the more motionally restricted population of spin labels (component 1) is found to arise when the spin label is hydrogen-bonded to the polar surfaces of the membranes, while the less motionally restricted population (component 2) is generated by spin labels nonhydrogen-bonded and more deeply inserted in the hydrophobic core. The 5-DSA is bound tightly to the polar surfaces (DeltaG(o)2 --> 1=-1.75 kcal/mol and DeltaH(o)2 --> 1=-13.8 kcal/mol), whereas the more lipophilic 5-DMS has a major spin population stabilized in the hydrophobic core (DeltaG(o)2 --> 10.57 kcal/mol and DeltaH(o)2 --> 1=-9.1 kcal/mol). Upon lipid-depleting SC increases the interactions of the probe with the polar surfaces, thereby decreasing its rotational diffusion. In contrast, the treatment of SC with oleic acid, a permeation enhancer, drastically increases the mobility of the spin labels, particularly that of component 1, and the thermodynamic equilibrium shifts towards the formation of component 2. A mechanism for water permeation in SC is also proposed.

Animals↗
PubMed1980

Electron spin resonance spin-label studies of mouse olfactory epithelium.

Three classes of interaction of spin-labeled odors with olfactory membrane of mouse were identified by electron spin resonance spectroscopy and correlated with the olfactory potencies of those odors. Also, variation of fluidity in this membrane was probed using spin-labeled lipids in which the nitroxide group was at increasing distances from the lipid headgroup. A cooperative model of olfactory transduction in agreement with the results is introduced, and typical dose response curves are computed that can predict molecular features necessary for a strong odor.

Acetaldehyde↗
PubMed1980

Synthesis of peptide spin-labels that bind to neurophysin and their application to distance measurements within neurophysin complexes.

The synthesis of two spin-labels capable of binding to the hormone-binding site(s) of neurophysin is described. The two spin-labels are 4-(glycyl-L-phenylalanylamido)-2,2,6,6-tetramethylpiperidinyl-1-oxy and S-[[[3-(2,2,5,5-tetramethylpyrrolidine-1-oxy)amino]carbonyl]methyl]-L-cysteinyl -L-tyrosine amide; synthesis of the former is achieved by a novel route to circumvent problems associated with nitroxide instability under standard conditions of peptide deblocking. NMR studies of the effects of binding these spin-labels on relaxation rates of individual proton resonances of neurophysin were used to calculate correlation times and distances between the bound nitroxides and the observed protons. The results indicate that residue 3 of peptides bound to the strong site of neurophysin is greater than or equal to 14 A from Tyr-49 and argue against a distance of < 5 A between the ortho ring protons of Tyr-49 and those of residue 2 of peptides bound to the strong site. Alternatively, the data suggest that the previously observed nuclear Overhauser effect between these protons reflects spin diffusion at the strong site and a contribution of uncertain magnitude from a second but very weak binding site; this second site is close to Tyr-49 and is detected by the increased relaxation rate of Tyr-49 ring protons when 4-(glycyl-L-phenylalanylamido)-2,2,6,6-tetramethylpiperidinyl-1-oxy is displaced from the strong site by competing diamagnetic peptide. Additionally, the data indicate that residue 3 of bound peptides at the strong site is distant from His-80 but approximately 12 A from the amino terminus. The extended side chain of residue 1 of peptides at the strong site is calculated as less than or equal to 10 A from Tyr-49.

Animals↗
PubMed2003

Membrane-docking loops of the cPLA2 C2 domain: detailed structural analysis of the protein-membrane interface via site-directed spin-labeling.

C2 domains are protein modules found in numerous eukaryotic signaling proteins, where their function is to target the protein to cell membranes in response to a Ca(2+) signal. Currently, the structure of the interface formed between the protein and the phospholipid bilayer is inaccessible to high-resolution structure determination, but EPR site-directed spin-labeling can provide a detailed medium-resolution view of this interface. To apply this approach to the C2 domain of cytosolic phospholipase A(2) (cPLA(2)), single cysteines were introduced at all 27 positions in the three Ca(2+)-binding loops and labeled with a methanethiosulfonate spin-label. Altogether, 24 of the 27 spin-labeled domains retained Ca(2+)-activated phospholipid binding. EPR spectra of these 24 labeled domains obtained in the presence and absence of Ca(2+) indicate that Ca(2+) binding triggers subtle changes in the dynamics of two localized regions within the Ca(2+)-binding loops: one face of the loop 1 helix and the junction between loops 1 and 2. However, no significant changes in loop structure were detected upon Ca(2+) binding, nor upon Ca(2+)-triggered docking to membranes. EPR depth parameters measured in the membrane-docked state allow determination of the penetration depth of each residue with respect to the membrane surface. Analysis of these depth parameters, using an improved, generalizable geometric approach, provides the most accurate picture of penetration depth and angular orientation currently available for a membrane-docked peripheral protein. Finally, the observation that Ca(2+) binding does not trigger large rearrangements of the membrane-docking loops favors the electrostatic switch model for Ca(2+) activation and disfavors, or places strong constraints on, the conformational switch model.

Amino Acid Substitution↗
PubMed1980

Spin-labelling of phosphorylase b using a paramagnetic 1-fluoro-2,4-dinitrobenzene derivative.

Phosphorylase b (1,4-alpha-D-glucan:1,6-alpha-D-glucan 6-alpha-glucosyltransferase, EC 2.4.1.1) can be specifically spin-labelled at a site essential for the catalytic action of the enzyme. A paramagnetic analogue of 1-fluoro-2,4-dinitrobenzene was synthesized and used as a dinitrophenylating agent. Reaction of phosphorylase b with the paramagnetic probe combined with the thiolysis method, leads to spin-labelling of a single -NH2 group (0.75 groups per subunit) with concomitant loss of 50% of the catalytic activity. Dinitrophenylation does not change the sedimentation profile of the enzyme. The ESR spectrum of modified phosphorylase b indicates that the attached label has rather limited segmental mobility and its environment is slightly hydrophobic. Small but subtle conformational changes induced by ligands in this critical site of the macromolecule can be directly detected by the spin-label. Also, sulfhydryl group modification of the spin-labelled enzyme with 5,5'-dithiobis(2-nitrobenzoic acid) has a pronounced effect on the resonance spectrum.

Animals↗
PubMed2002

Site-directed spin labeling of a bacterial chemoreceptor reveals a dynamic, loosely packed transmembrane domain.

We used site-directed spin labeling and electron paramagnetic resonance spectroscopy to investigate dynamics and helical packing in the four-helix transmembrane domain of the homodimeric bacterial chemoreceptor Trg. We focused on the first transmembrane helix, TM1, particularly on the nine-residue sequence nearest the periplasm, because patterns of disulfide formation between introduced cysteines had identified that segment as the region of closest approach among neighboring transmembrane helices. Along this sequence, mobility and accessibility of the introduced spin label were characteristic of loosely packed or solvent-exposed side chains. This was also the case for eight additional positions around the circumference and along the length of TM1. For the continuous nine-residue sequence near the periplasm, mobility and accessibility varied only modestly as a function of position. We conclude that side chains of TM1 that face the interior of the four-helix domain interact with neighboring helices but dynamic movement results in loose packing. Compared to transmembrane segments of other membrane proteins reconstituted into lipid bilayers and characterized by site-directed spin labeling, TM1 of chemoreceptor Trg is the most dynamic and loosely packed. A dynamic, loosely packed chemoreceptor domain can account for many experimental observations about the transmembrane domains of chemoreceptors.

Diffusion↗
PubMed2003

In vivo assessment of absolute perfusion in the murine skeletal muscle with spin labeling MRI. Magnetic resonance imaging.

PURPOSE: To assess absolute perfusion in the skeletal muscle of mice in vivo with spin labeling magnetic resonance imaging (MRI) under normal and stress conditions. MATERIALS AND METHODS: Absolute perfusion in the skeletal muscle of 27 C57BL/6 mice was assessed in vivo non-invasively by spin labeling MRI at 7.05 T. This technique was based on the acquisition of T1 maps with global and slice-selective spin inversion in separate acquisitions. T1 mapping was performed by inversion recovery snapshot fast low angle shot imaging. To guarantee proper spin inversion within the whole mouse, a dedicated radiofrequency (RF) coil combination was constructed. A birdcage resonator was used for transmission, while detection of the MRI signal was achieved by a surface coil. RESULTS: Basal perfusion in the hindlimbs was determined to be 94 +/- 10 mL (100 g x minute)(-1) (mean +/- standard error of the mean [SEM], N = 27). This value is in good agreement with perfusion values determined by invasive techniques such as microspheres. A subgroup of six animals received a constant dose of 4 mg (kg x minute)(-1) of the vasodilator adenosine by an intraperitoneal catheter. In this case, perfusion was significantly increased to 179 +/- 56 mL (100 g x minute)(-1) (mean +/- SEM, N = 6, P < 0.02). Mean basal perfusion in this subgroup was 96 +/- 26 mL (100 g x minute)(-1). CONCLUSION: Spin labeling MRI is a well-suited technique for the in vivo assessment of absolute perfusion in the murine skeletal muscle.

Adenosine↗
PubMed1992

Spin-labeling studies of the conformation of the Ca(2+)-regulatory protein calmodulin in solution and bound to the membrane skeleton in erythrocyte ghosts: implications to transmembrane signaling.

Electron paramagnetic resonance (EPR) studies of the Ca(2+)-regulatory protein calmodulin (CaM) have been performed. The conformation of CaM in solution changes upon binding of Ca2+ allowing the protein to bind to target proteins existing in the red blood cell membrane. In this study a maleimide spin label, covalently attached to the single cysteine residue of CaM located in the first Ca(2+)-binding domain, was used to monitor allosteric conformational changes induced by interaction of CaM with Ca2+ and subsequently with the red blood cell membrane. The results show, relative to apo-CaM, a significant increase in the apparent rotational correlation time, tau, of the spin label when Ca2+ was present in solution (P less than 0.001). When apo-CaM exposed to red blood cell membrane ghosts in the absence of Ca2+, no significant difference in spin label motion was seen relative to solution, consistent with the idea that Ca2+ is required for CaM to bind to skeletal proteins. When Ca2+ was added to CaM which was then exposed to ghosts, a highly significant increase in tau (decrease in motion) (P less than 0.000001) relative to apo-CaM exposed to ghosts was found. This latter increase in tau is significantly greater than that produced by the addition of Ca2+ to CaM in solution (P less than 0.001). The major interaction sites of CaM were found by photoaffinity labeling and autoradiography on SDS-PAGE to be on the principal skeletal protein, spectrin. EPR was also used to investigate the biophysical correlates of transmembrane signaling. Spin-labeled CaM was bound to the membrane skeleton in the presence of Ca2+. On the opposite side of the erythrocyte membrane a lectin was bound to the external glycoconjugate of Band 3, the major transmembrane protein of the erythrocyte. A highly significant increase in T of the maleimide spin probe was found relative to the control system in which the lectin was absent. (P < 0.00001). These results suggest that electron paramagnetic resonance spectra of spin-labeled CaM can provide useful information about protein structure and function when in solution and when bound to membranes.

Autoradiography↗
PubMed1988

Comparative spin-label study of the dynamic structure of human hemoglobins A and F and the influence of the antibiotic, chloramphenicol.

Hemoglobin A (HbA) and hemoglobin F (HbF) dynamic structures have been studied using spin-label ESR spectra analysis technique, which permits quantitative separation of slow macromolecular rotation (described by rotational correlation time, tau c) and fast anisotropic nitroxide radical motion (described by the 'order parameter', S). The hardly restricted motion of the maleimide spin-label reflects the overall macromolecular rotation and small dynamic structure differences between HbA and HbF were observed (tau c is equal to 26 and 27 ns, respectively). On the other hand, the dynamic equilibrium of the iodoacetamide spin-label demonstrates significant differences between beta- and gamma-chain C-terminus flexibility. Thus, there are different states of alpha,beta and alpha,gamma intersubunit contacts which may be expected to determine the different O2 affinity of HbA and HbF. The antibiotic, chloramphenicol, strongly affects the O2 affinity and the Hill constant of HbF, and also provides detectable changes of gamma-subunit C-terminus flexibility (tau c changes from 20 ns to 27 ns after chloramphenicol treatment of HbF), while the HbA tetramer structure remains almost unaffected. The HbF domain structure rearrangements are accompanied by a decrease of the steric restriction of the spin-label motion (S changes from 0.75 to 0.72).

Adult↗
PubMed2005

Synthesis of spin-labeled RNAs for long range distance measurements by peldor.

Site directed spin labeled RNA duplexes with different interspin distances were synthesized. The radical 2,2,5,5-tetramethyl-pyrrolin- 1-yloxyl-3-acetylene (TPA) was introduced during the solid-phase synthesis through a Sonogashira cross-coupling with 5-iodo-uridine. Tm and CD studies showed that the spin label does not to disturb significantly the A-form of these duplexes. 4-Pulse Electron Double Resonance (PELDOR) was then used to measure intramolecular spin-spin distances of 19.3, 33.0 and 40.9 A, which are in very good agreement with the calculated values of 17.6, 32.1 and 39.1 A, obtained from Molecular Dynamics (MD) simulations.

Biochemistry↗