Phosphorus-31 studies on lecithin in ethanol solutions

³¹P relaxation times of lecithin in ethanol solutions have been measured in dependence on temperature and water concentration. Trial calculations have been carried out on the assumption of a 2-site exchange model. The results suggest first, the relaxation behaviour is determined by various motional and exchange processes; second, at 29 MHz the dipole-dipole interaction between ³¹P and protons provides the dominant contribution; third, in general we are not concerned with the case of “extreme narrowing”. Moreover, there are no negligible intermolecular contributions to relaxation.     

Individual residue correlation times of peptides from proton relaxation parameters: application to gramicidin S.

Three ¹H nmr relaxation methods are presented for determining the correlation times of interproton vectors in peptides and proteins. Within experimental error a single correlation time, 11 × 10^?10 sec., is found for the backbone interproton vectors in gramicidin S. These methods are generally applicable to the measurement of side chain and backbone motional rates of peptides and other biopolymers and can be used for determinations of interproton distances from ¹H nuclear Overhauser effects.     

15N spin-lattice relaxation study of linear peptides: Preliminary results on Leu-enkephalin and Tyr-Gly-Gly-Phe

The ability of ¹⁵N relaxation measurements in conformational analysis of linear peptides was studied using Leu-enkephalin: Tyr-Gly-Gly-Phe-Leu and and related tetrapeptide Tyr-Gly-Gly-Phe 95 % ¹⁵N enriched. ¹⁵N spin-lattice relaxation times measured at different temperatures in Me₂SO solution indicate the presence of highly preferential folded structures in both peptides. A marked dependence of T₁ upon the motional effects (segmental rather than anisotropic overall) was observed, while hydrogen bonding affects weakly the relaxation times. From a comparison of ¹⁵N relaxation parameters it appears that the tetrapeptide exhibits a more rigid structure than Leu-enkephalin, in accordance with previous ¹H NMR studies. This paper provides evidence for the usefulness of ¹⁵N T₁ as a mobility probe (independent from ¹³C) in the investigation of the conformational dynamics of peptides.     

A possible role for melatonin in regulation of chick liver xanthine dehydrogenase activity.

³⁵Cl nuclear magnetic resonance longitudinal and transverse relaxation times were employed to study anion binding to rabbit muscle lactate dehydrogenase. The correlation time, obtained from a comparison of the two relaxation times, shows that coenzyme has a marked retarding effect on the anion mobility at the binding site. The quadrupole coupling constant is estimated from the magnitude of the relaxation rate change on oxamate addition.     

Protein dynamics in supercooled water: the search for slow motional modes

The impact of studying protein dynamics in supercooled water for identifying slow motional modes on the s time scale is demonstrated. Backbone ¹⁵N spin relaxation parameters were measured at –13°C for ubiquitin, which plays a central role for signaling proteolysis, cellular trafficking and kinase activation in eukaryotic organisms. A hitherto undetected motional mode involving Val 70 was found, which may well play an important role for ubiquitin recognition. The measurement of rotating frame ¹⁵N relaxation times as a function of the spin-lock field allowed determination of the correlation time of this motional mode, which would not have been feasible above 0°C.     

Interaction of the antimalarial drug fluoroquine with DNA,tRNA, and poly(A): 19F-NMR chemical-shift and relaxation,optical absorption,and fluorescence studies

The interaction of the fluorinated antimalarial drug fluoroquine [7-fluoro-4-(diethyl-amino-1-methylbutylamino)quinoline] with DNA, tRNA, and poly(A) has been investigated by optical absorption, fluorescence, and ¹⁹F-nmr chemical-shift and relaxation methods. Optical absorption and fluorescence experiments indicate that fluoroquine binds to nucleic acids in a similar manner to that of its well-known analog chloroquine. At low drug-to-base pair ratios, binding of both drugs appears to be random. Fluoroquine and chloroquine also elevate the melting temperature (T_m) of DNA to a comparable extent. Binding of fluoroquine to DNA, tRNA, or poly(A) results in a downfield shift of about 1.5 ppm for the ¹⁹F-nmr resonance. The chemical shift of free fluoroquine depends on the isotopic composition of the solvent (D₂O vs H₂O). The solvent isotope shift is virtually eliminated by fluoroquine binding to any one of the nucleic acids. ¹⁹F-nmr relaxation experiments were carried out to measure the spin-lattice relaxation time (T₁), ¹⁹F{¹H} nuclear Overhauser effect (NOE), off-resonance intensity ratio (R), off-resonance rotating-frame spin-lattice relaxation time (T), and linewidth for fluoroquine in the nucleic acid complexes. By accounting for intramolecular proton-fluorine dipolar and chemical-shift anisotropy contributions to the fluorine relaxation, all of the relaxation parameters for the fluoroquine–DNA complex can be well described by a motional model incorporating long-range DNA bending on the order of a microsecond and an internal motion of the drug on the order of a nanosecond. Selective NOE experiments indicate that the fluorine in the drug is near the ribose protons in the RNA complexes, but not in the DNA complex. Details of the binding evidently differ for the two types of nucleic acids. This study provides the foundation for an investigation of fluoroquine in intact cells.     

Quantitative analysis of backbone motion in proteins using MAS solid-state NMR spectroscopy

We present a comprehensive analysis of protein dynamics for a micro-crystallin protein in the solid-state. Experimental data include ¹⁵N T ₁ relaxation times measured at two different magnetic fields as well as ¹H–¹⁵N dipole, ¹⁵N CSA cross correlated relaxation rates which are sensitive to the spectral density function J(0) and are thus a measure of T ₂ in the solid-state. In addition, global order parameters are included from a ¹H,¹⁵N dipolar recoupling experiment. The data are analyzed within the framework of the extended model-free Clore–Lipari–Szabo theory. We find slow motional correlation times in the range of 5 and 150 ns. Assuming a wobbling in a cone motion, the amplitude of motion of the respective amide moiety is on the order of 10° for the half-opening angle of the cone in most of the cases. The experiments are demonstrated using a perdeuterated sample of the chicken α-spectrin SH3 domain.     

Molecular dynamics through 2H spin-lattice relaxation time measurements within an enzyme-inhibitor complex: Lysozyme and methyl N-acetyl glucosamin

Deuteron spin-lattice relaxation times of specifically labelled methyl N-acetyl-D-glucosaminides associated to lysozyme were measured from ¹H and ²H NMR spectra through bandshape analysis and FT inversion-recovery technique, respectively. Model calculations were carried out in order to assess the limits of the extreme narrowing approximation for the systems studied. Rotational correlation times of the acelamido methyl groups were analyzed in terms of anisolropic overall reorientation combined with internal rotation. The acetamido methyl group undergoes fast internal rotation in the α-glycoside complex about an axis nearly parallel with the major ellipsoidal axis of lysozyme. More rotational freedom is likely to occur in the β-glycoside complex.     

Hydration dependent dynamics in RNA

The essential role played by local and collective motions in RNA function has led to a growing interest in the characterization of RNA dynamics. Recent investigations have revealed that even relatively simple RNAs experience complex motions over multiple time scales covering the entire ms–ps motional range. In this work, we use deuterium solid-state NMR to systematically investigate motions in HIV-1 TAR RNA as a function of hydration. We probe dynamics at three uridine residues in different structural environments ranging from helical to completely unrestrained. We observe distinct and substantial changes in ²H solid-state relaxation times and lineshapes at each site as hydration levels increase. By comparing solid-state and solution state ¹³C relaxation measurements, we establish that ns–μs motions that may be indicative of collective dynamics suddenly arise in the RNA as hydration reaches a critical point coincident with the onset of bulk hydration. Beyond that point, we observe smaller changes in relaxation rates and lineshapes in these highly hydrated solid samples, compared to the dramatic activation of motion occurring at moderate hydration.     

Solution conformation and dynamics of a tetrasaccharide related to the LewisX antigen deduced by NMR relaxation measurements

¹H-NMR cross-relaxation rates and nonselectivelongitudinal relaxation times have been obtained at two magnetic fields (7.0and 11.8 T) and at a variety of temperatures for the branchedtetrasaccharide methyl3-O--N-acetyl-galactosaminyl--galactopyranosyl-(14)[3-O--fucosyl]-glucopyranoside (1), an inhibitor of astrocyte growth. Inaddition, ¹³C-NMR relaxation data have also been recorded atboth fields. The ¹H-NMR relaxation data have been interpretedusing different motional models to obtain proton–proton correlationtimes. The results indicate that the GalNAc and Fuc rings display moreextensive local motion than the two inner Glc and Gal moieties, since thosepresent significantly shorter local correlation times. The¹³C-NMR relaxation parameters have been interpreted in termsof the Lipari–Szabo model-free approach. Thus, order parameters andinternal motion correlation times have been deduced. As obtained for the¹H-NMR relaxation data, the two outer residues possess smallerorder parameters than the two inner rings. Internal correlation times are inthe order of 100 ps. The hydroxymethyl groups have also different behaviour,with the exocyclic carbon on the glucopyranoside unit showing the highestS². Molecular dynamics simulations using a solvated systemhave also been performed and internal motion correlation functions have beendeduced from these calculations. Order parameters and interproton distanceshave been compared to those inferred from the NMR measurements. The obtainedresults are in fair agreement with the experimental data.     

Diffusion and dynamics of penetratin in different membrane mimicking media

The interaction between the cell-penetrating peptide (CPP) penetratin and different membrane mimetic environments has been investigated by two different NMR methods: ¹⁵N spin relaxation and translational diffusion. Diffusion coefficients were measured for penetratin in neutral and in negatively charged bicelles of different size, in sodium dodecyl sulfate micelles (SDS), and in aqueous solution. The diffusion coefficients were used to estimate the amount of free and bicelle/micelle-bound penetratin and the results revealed that penetratin binds almost fully to all studied membrane mimetics. ¹⁵N relaxation data for three sites in penetratin were interpreted with the model-free approach to obtain overall and local dynamics. Overall correlation times for penetratin were in agreement with findings for other peptides of similar size in the same solvents. Large differences in order parameters were observed for penetratin in the different membrane mimetics. Negatively charged surfaces were seen to restrict motional flexibility, while a more neutral membrane mimetic did not. This indicates that although the peptide binds to both bicelles and SDS micelles, the interaction between penetratin and the various membrane mimetics is different.     

13C NMR studies on fluorescent probes: 13C chemical shifts and longitudinal relaxation times of n-hydroxy-fatty (n=2,6,9,12) acids and n-(9-anthroyloxy)-stearic (n=6,12) acids

¹³C NMR has been used to confirm the structure of two fluorescent probes, n-(9-anthroyloxy)-stearic acids (n=6,12), and the series of n-hydroxy-fatty acids (n=2,6,9,12) from which the set of fluorescent fatty acids may be synthesised. ¹³C longitudinal relaxation times and correlation times of the individual carbon atoms in 12-hydroxy- and 6- and 12-(9-anthroyloxy)-stearic acids show differences in motional properties between these derivatives and the parent stearic acid in chloroform(d) solution. The correlation times of the substituted carbons in 6-, 9-, and 12-hydroxy-stearic acids are longer than the corresponding carbons in stearic acid. The change in correlation times at the substituted carbons reflects the increase in motion along the acyl chain. Attachment of the bulky anthracene ring causes greater restriction of motion at the substituted carbon atom but the gradient of motion along the chain is preserved. These results are discussed in terms of the types of motion which lead to fluorescence depolarization when the fluorescent fatty acids are used as fluidity probes in biomembranes.     

Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy

We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline α-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual ¹⁵N–T ₁ timescales). We observed chemical exchange for 6 residues with HDX exchange rates in the range from 0.2 to 5 s⁻¹. Backbone amide ¹⁵N longitudinal relaxation times that we determined previously are not significantly affected for most residues, yielding no systematic artifacts upon quantification of backbone dynamics (Chevelkov et al. 2008b). Significant exchange was observed for the backbone amides of R21, S36 and K60, as well as for the sidechain amides of N38, N35 and for W41ε. These residues could not be fit in our previous motional analysis, demonstrating that amide proton chemical exchange needs to be considered in the analysis of protein dynamics in the solid-state, in case D₂O is employed as a solvent for sample preparation. Due to the intrinsically long ¹⁵N relaxation times in the solid-state, the approach proposed here can expand the range of accessible HDX rates in the intermediate regime that is not accessible so far with exchange quench and MEXICO type experiments.     

DNA replication of SV40-infected cells. VII. Formation of SV40 catenated and circular dimers

The binding of methyl isonitrile (CH₃Nandz.tbnd;C) to hemoglobin β chains has been studied by measuring the ¹H nuclear magnetic resonance transverse relaxation times for methyl isonitrile as a function of protein concentration, temperature and ¹⁴N decoupling. Binding of methyl isonitrile both at the heme iron and at a non-specific site (or sites) has an effect upon the measured nuclear spin relaxation times. The results yield a value of 57 ± 12 seconds^?1 (20 °C) for the “off” rate constant K_?1 for specific binding and an Arrhenius activation energy for k_?1 of 14 ± 3 kcal mol^?1.     

Protein dynamics studied by rotating frame 15N spin relaxation times

Summary Conformational rate processes in aqueous solutions of uniformly ¹⁵N-labeled pancreatic trypsin inhibitor (BPTI) at 36°C were investigated by measuring the rotating frame relaxation times of the backbone ¹⁵N spins as a function of the spin-lock power. Two different intramolecular exchange processes were identified. A first local rate process involved the residues Cys³⁸ and Arg³⁹, had a correlation time of about 1.3 ms, and was related to isomerization of the chirality of the disulfide bond Cys¹⁴-Cys³⁸. A second, faster motional mode was superimposed on the disulfide bond isomerization and was tentatively attributed to local segmental motions in the polypeptide sequence-Cys¹⁴-Ala¹⁵-Lys¹⁶-. The correlation time for the overall rotational tumbling of the protein was found to be 2 ns, using the assumption that relaxation is dominated by dipolar coupling and chemical shift anistropy modulated by isotropic molecular reorientation.Abbreviations BPTI basic pancreatic trypsin inhibitor - 2D two-dimensional - COSY 2D correlation spectroscopy - TOCSY 2D total correlation spectroscopy - RF radio frequency - CW continuous wave - TPPI time-proportional phase incrementation - CSA chemical shift anisotropy - T₁ longitudinal relaxation time - T₂ transverse relaxation time - T₁ relaxation time in the rotating frame , correlation time for overall rotational reorientation of the protein - _ex ^s , _ex ^f , correlation times for two conformational exchange processes (slow and fast).     

An NMR spectroscopy study of bendaline-albumin interactions

The complete assignment of the 1H and 13C NMR spectra of bendaline (BNDL) was performed by mono-dimensional and homo- and hetero-correlated two-dimensional NMR experiments. The interaction between bendaline and albumin was also studied by the analysis of the motional parameters spin-lattice relaxation times, allowing the motional state of the BNDL free and bound with albumin to be defined. In absence of albumin the indazolacetic and benzylic moieties are characterized by roughly the same mobility and by positive sigma (cross-relaxation rates) values. In the presence of the macromolecule, the indazolacetic and benzylic moieties and the lysine change their motional behaviour to different extents, as indicated by correlation times. Data obtained in absence and in presence of the protein show that the molecular moiety of the bendaline most involved in the binding with albumin is the fragment H-4 H-5. The binding constant was evaluated at 2.4x10(3)M(-1).     

Internal motions studies of an angiotensin pentapeptide using proton relaxation parameters.

We report mono and bi-selective excitation proton relaxation studies of internal motion of three side chaing in a peptide fragment of angiotensin of sequence Tyr¹. Ile². His³. Pro⁴. Phe⁵. The motion of this peptide does not satisfy the extreme narrowing conditions and the general approach to the interpretation of proton relaxation rates given here can be used in larger peptides and proteins.     

Direct observation of the properties of cholesterol in membranes by deuterium NMR

The properties of cholesterol in bilayers of egg phosphatidylcholine (PC) were investigated directly by means of ²H-NMR of specifically-deuterated species (C3, C7, C26, C27). Quadrupole splittings were a measure of molecular ordering, and relaxation times T₁ and T_2e were indicators of rates of motion. The importance of the use of echoes for spectral acquisition is emphasised, particularly to obtain accurate values of the quadrupole splitting. In the case of overlapping powder patterns from two labelled positions, the use of the absolute value mode of spectral presentation is shown to yield reasonable estimates of the individual quadrupole splittings. Spectral properties were monitored as a function of cholesterol concentration and temperature. Increasing cholesterol concentration led to a high degree of ordering for the rigid ring system of cholesterol, approaching a molecular order parameter of 0.8 at 50 mol% cholesterol. The isopropyl methyl groups were in all cases less ordered anmore mobile than the ring system, but responded in a similar fashion to variable cholesterol concentration and temperature. The observation of a minimum in the temperature dependence of T₁ for cholesterol-7,7-d₂ led to a direct estimate of its correlation time for molecular motion, 3.5 × 10^?9 s rad^?1. This indicates that the overall rate of motion of cholesterol is considerably slower than that of the lipids in which it is located. The short T_2e values suggest that the motional spectrum of cholesterol is rich in low frequencies. The parallel temperature and cholesterol dependences of quadrupole splittings for different positions on the rigid ring system of cholesterol indicate that the position of the axis of motional averaging of the molecule is not changing, and is the same as that determined in an earlier study. It is emphasised that the steep temperature dependence and small quadrupole splittings for the chain isopropyl methyl groups of cholesterol do not necessarily indicate a high degree of disorder, but may be due to their axes of motional averaging lying at angles close to 54° with respect to the director of the ordered lipids.     

Pulsed nuclear magnetic resonance studies on 23 Na, 7 Li and 35 Cl binding to human oxy- and carbon monoxyhaemoglobin

Pulsed nuclear magnetic resonance studies of the longitudinal (T₁) and transverse (T₂) quadrupolar relaxation times of ⁷Li, ²³Na, ³⁵Cl ions in the absence and presence of human oxy- and carbon monoxyhaemoglobin have been used to investigate the interaction of the ions and the macromolecule.The relaxation data show that Cl^? interacts strongly with the haemoglobin but provide no evidence for binding of Na⁺ up to concentrations of 0.5 m. In the case of Li⁺, evidence for interaction is obtained at concentrations of about 0.1 m.The dependence of relaxation rate on frequency was followed over a limited frequency range in an attempt to separate the effects of correlation times and exchange rates of the bonded ions on the relaxation. In the case of Cl^?, an upper limit for the mean lifetime divided by the number of sites can be set at about 1 × 10^?6 second, and a lower limit at about 1 × 10^?8 second.