Backbone dynamics of proteins derived from carbonyl carbon relaxation times at 500, 600 and 800 MHz: Application to ribonuclease T1

The backbone dynamics of uniformly 13C/15N-enriched ribonuclease T1 have beeninvestigated using carbonyl carbon relaxation times recorded at three different spectrometerfrequencies. Pulse sequences for the determination of the longitudinal (T1) and transverse (T2)relaxation times are presented. The relaxation behaviour was analysed in terms of a multispinsystem. Although the chemical shift anisotropy relaxation mechanism dominates at highmagnetic field strength, the contributions of the dipole–dipole interactions and thecross-correlation between these two relaxation mechanisms have also been considered.Information about internal motions has been extracted from the relaxation data using themodel-free approach of Lipari and Szabo in order to determine order parameters (S2) andeffective internal correlation times (i). Using a relatively simple relation between themeasured relaxation rates and the spectral density function, an analytical expression for themicrodynamical parameters in dependence of T1 and T2 has been derived. The spectraldensity mapping technique has been applied in order to study the behaviour of the carbonylcarbon resonances in more detail.     

Kinetics of allosteric conformational transition of a macromolecule prior to ligand binding

Two fundamentally different mechanisms of ligand binding are commonly encountered in biological kinetics. One mechanism is a sequential multistep reaction in which the bimolecular binding step is followed by first-order steps. The other mechanism includes the conformational transition of the macromolecule, before the ligand binding, followed by the ligand binding process to one of the conformational states. In stopped-flow kinetic studies, the reaction mechanism is established by examining the behavior of relaxation times and amplitudes as a function of the reactant concentrations. A major diagnostic tool for detecting the presence of a conformational equilibrium of the macromolecule, before the ligand binding, is the decreasing value of one of the reciprocal relaxation times with the increasing [ligand]. The sequential mechanism cannot generate this behavior for any of the relaxation times. Such dependence is intuitively understood on the basis of approximate expressions for the relaxation times that can be comprehensively derived, using the characteristic equation of the coefficient matrix and polynomial theory. Generally, however, the used approximations may not be fulfilled. On the other hand, the two kinetic mechanisms can always be distinguished, using the approach based on the combined application of pseudo-first-order conditions, with respect to the ligand and the macromolecule. The two experimental conditions differ profoundly in the extent of the effect of the ligand on the protein conformational equilibrium. In a large excess of the ligand, the conformational equilibrium of the macromolecule, before the ligand binding, is strongly affected by the binding process. However, in a large excess of the macromolecule, ligand binding does not perturb the internal equilibrium of the macromolecule. As a result, the normal mode, affected by the conformational transition, is absent in the observed relaxation process. In the case of a sequential mechanism, the number of relaxation times is not altered by different pseudo-first-order conditions. Thus, the approach provides a strong diagnostic criterion for detecting the presence of the conformational transition of the macromolecule and establishing the correct mechanism. Application of this approach is illustrated for the binding of 3'-O-(N-methylantraniloyl)-5'-diphosphate to the E. coli DnaC protein.     

High-frequency ultrasonic absorption spectroscopy on aqueous suspensions of phospholipid bilayer vesicles

Between 1 MHz and 3 GHz the ultrasonic absorption coefficient has been precisely measured as a function of frequency for some aqueous suspensions of single-walled phospholipid bilayer vesicles. All solutions of the specially purified phospholipids clearly show excess absorption, reflecting three molecular relaxation processes with discrete relaxation times. Typical values for these times are 50, 3 and 0.5 ns. The attempt is made to relate these relaxation processes to mechanisms of rotational isomerization in the hydrocarbon chains. Some other molecular mechanisms which could also contribute to the ultrasonic excess absorption spectra are also briefly discussed.     

Determination of kinetic parameters from chemical relaxation data discrimination between coupled two-step binding reactions differing in stoichiometry

The chemical relaxation times of two different two-step equilibrium reactions, characterized by a 1:1 binding process followed by a subsequent rearrangement step and a stepwise 1:2 binding reaction, are analyzed for the purpose of qualitative model discrimination and quantitative determination of kinetic parameters. The equations describing the dependences of the two reciprocal relaxation times on suitable concentrations are given for both models in the general case as well as for four different limiting situations which are characterized by well separated relaxation times. The conditions corresponding to the limiting cases are expressed in terms of strong, weak and no coupling between the two partial equilibrium steps involved in both models. The coupling strength depends on the rate constants as well as on the total concentrations of the reactants. Criteria to discriminate between these two reaction models under defined limiting conditions are developed. In the general case, the product of both reciprocal relaxation times can be used to distinguish both models. If only one relaxation time can be resolved experimentally, it is possible under conditions described to determine only a reduced set of individual rate constants for most of the limiting cases considered. If both relaxation times are observed, all rate constants are determinable in the general case as well as in most of the limiting cases discussed.     

Proton magnetic relaxation dispersion in solutions of the cuproprotein diamine oxidase.

Proton nuclear magnetic resonance relaxation measurements were made over the range 4.7--220 MHz for aqueous solutions of hog kidney diamine oxidase. The values of 1/T1 give rise in two distinct dispersions, at 16 and 75 MHz, whereas 1/T2 displays a minimum at 20 MHz. The temperature dependence of relaxation rates in all cases yield apparent activation energies less than 0.6 kcal/mol. These data indicate to us that the two Cu(II) ions of diamine oxidase are intrinsically different in terms of their electronic relaxation characteristics and hence, chemical environments. Low field limits of the two electronic relaxation times are 2 and 10 ns, with one of these correlation times being frequency dependent. The value of the frequency-dependent electronic relaxation time is governed by interactions that are modulated by a process having a correlation time of 5 ps.     

Nuclear Magnetic Resonance Transverse Relaxation Times of Water Protons in Skeletal Muscle

The observation of the spin-echo decay in a long time domain has revealed that there exist at least three different fractions of non- (or slowly) exchanging water in the rat gastrocnemius muscle. These fractions of water are characterized with different nuclear magnetic resonance (NMR) relaxation times and are identified with the different parts of tissue water. The water associated with the macromolecules was found to be approximately 8% of the total tissue water and not to exchange rapidly with the rest of the intracellular water. The transverse relaxation time (T₂) of the myoplasm is 45 ms which is roughly a 40-fold reduction from that of a dilute electrolyte solution. This fraction of water accounts for 82% of the tissue water. The reduced relaxation time is shown neither to be caused by fast exchange between the hydration and myoplasmic water nor by the diffusion of water across the local magnetic field gradients which arise from the heterogeneity in the sample. About 10% of the tissue water was resolved to be associated with the extracellular space, the relaxation time of which is approximately four times that of the myoplasm. Mathematical treatments of the proposed mechanisms which may be responsible for the reduction of tissue water relaxation times are given in this paper. The results of our study are consistent with the notion that the structure and/or motions of all or part of the cellular water are affected by the macromolecular interface and this causes a change in the NMR relaxation rates.     

Effect of neuromuscular electrical stimulation on motor cortex excitability upon release of tonic muscle contraction

The aim of the present study was to investigate the neurophysiological triggers underlying muscle relaxation from the contracted state, and to examine the mechanisms involved in this process and their subsequent modification by neuromuscular electrical stimulation (NMES). Single-pulse transcranial magnetic stimulation (TMS) was used to produce motor-evoked potentials (MEPs) and short-interval intracortical inhibition (SICI) in 23 healthy participants, wherein motor cortex excitability was examined at the onset of voluntary muscle relaxation following a period of voluntary tonic muscle contraction. In addition, the effects of afferent input on motor cortex excitability, as produced by NMES during muscle contraction, were examined. In particular, two NMES intensities were used for analysis: 1.2 times the sensory threshold and 1.2 times the motor threshold (MT). Participants were directed to execute constant wrist extensions and to release muscle contraction in response to an auditory “GO” signal. MEPs were recorded from the flexor carpi radialis (FCR) and extensor carpi radialis (ECR) muscles, and TMS was applied at three different time intervals (30, 60, and 90?ms) after the “GO” signal. Motor cortex excitability was greater during voluntary ECR and FCR relaxation using high-intensity NMES, and relaxation time was decreased. Each parameter differed significantly between 30 and 60?ms. Moreover, in both muscles, SICI was larger in the presence than in the absence of NMES. Therefore, the present findings suggest that terminating a muscle contraction triggers transient neurophysiological mechanisms that facilitate the NMES-induced modulation of cortical motor excitability in the period prior to muscle relaxation. High-intensity NMES might facilitate motor cortical excitability as a function of increased inhibitory intracortical activity, and therefore serve as a transient trigger for the relaxation of prime mover muscles in a therapeutic context.     

Relaxation studies of enzymes: concentration and pH dependence of isomerization phenomena.

Equations have been developed for the relaxation times for a variety of mechanisms involving enzyme isomerization coupled to proton transfers. The concentration and pH dependences of the relaxation time have been calculated and graphed for a number of representative mechanisms. We find that for most of the mechanisms examined, the relaxation time is not only pH but also strongly concentration dependent. The concentration dependence results from finite perturbations of the hydrogen ion concentration. For the systems tested, the relaxation time shows a clear concentration dependence at enzyme concentrations below 200 microM.     

On the flexibility of myosin in solution.

Rabbit skeletal muscle myosin from the same rabbit was prepared by two different methods, and then purified by either Sephadex or hydroxylapatite chromatography. The resulting myosin samples were analyzed in 2-10 mM sodium pyrophosphate solutions at pH 9 using transient electric birefringence. The birefringence decay signals were fitted using a Fortran program called DISCRETE and two relaxation times, 49.7 +/- 5.6 and 11.2 +/- 2.5 microseconds, were determined. These relaxation times were independent of the method of myosin preparation, the method of myosin purification, the concentration of sodium pyrophosphate between 2 and 10 mM, the concentration of myosin between 0.08 and 1.59 mg/mL, and the temperature between 4.0 and 20.0 degrees C, after correction to 20.0 degrees C. The longer relaxation time is consistent with a rigid, linear myosin molecule. The shorter relaxation time is consistent with myosin that has a completely flexible hinge region in the myosin tail. Both relaxation times are inconsistent with the previously reported single relaxation time of myosin obtained by fitting the birefringence decay data to only 90% of the decay signal. By forcing some of the birefringence decay data in the presence work to fit 90% of the decay signal with a single relaxation time, approximately the same relaxation time as previously reported was obtained.     

Calcium-dependent changes in the flexibility of the regulatory domain of troponin C in the troponin complex

With the recent advances in structure determination of the troponin complex, it becomes even more important to understand the dynamics of its components and how they are affected by the presence or absence of Ca(2+). We used NMR techniques to study the backbone dynamics of skeletal troponin C (TnC) in the complex. Transverse relaxation-optimized spectroscopy pulse sequences and deuteration of TnC were essential to assign most of the TnC residues in the complex. Backbone amide (15)N relaxation times were measured in the presence of Ca(2+) or EGTA/Mg(2+). T(1) relaxation times could not be interpreted precisely, because for a molecule of this size, the longitudinal backbone amide (15)N relaxation rate due to chemical shift anisotropy and dipole-dipole interactions becomes too small, and other relaxation mechanisms become relevant. T(2) relaxation times were of the expected magnitude for a complex of this size, and most of the variation of T(2) times in the presence of Ca(2+) could be explained by the anisotropy of the complex, suggesting a relatively rigid molecule. The only exception was EF-hand site III and helix F immediately after, which are more flexible than the rest of the molecule. In the presence of EGTA/Mg(2+), relaxation times for residues in the C-domain of TnC are very similar to values in the presence of Ca(2+), whereas the N-domain becomes more flexible. Taken together with the high flexibility of the linker between the two domains, we concluded that in the absence of Ca(2+), the N-domain of TnC moves independently from the rest of the complex.     

Relaxation kinetics of DNA-ligand binding including direct transfer

The relaxation kinetics of binding of ethidium to calf-thymus DNA as studied previously by the temperature-jump method with absorption detection [Bresloff, J. & Crothers, D. M. (1975) J. Mol. Biol. 95 , 103] is reanalyzed in terms of a series of models for DNA-ligand interactions that include cases with and without internal and bimolecular direct transfer of ligands between different binding modes or different binding sites. The experimental results are shown to be consistent with two alternative binding mechanisms. Both models include bimolecular “direct transfer” steps and a site size of two base pairs per site. In the first model, there exist two distinct modes of binding to the DNA double helix at each binding site. In the second model, sites containing at least one GC base pair constitute a different and stronger class of binding sites than those containing only AT base pairs. The existence of a direct transfer pathway between two classes of bound ligands is supported by the linear increase of reciprocal relaxation times far beyond the concentration regions, where off-rates should have become rate limiting. The second model, incorporating the notion of base selectivity, is in quantitative agreement with published work on ethidium binding to DNAs of different base compositions and with nmr measurements of bound ligand lifetimes.     

A temperature-jump study of the reaction between azurin and cytochrome c-551 from Pseudomonas aeruginosa (Short Communication)

Temperature-jump studies on the electron-transfer reaction between azurin and cytochrome c-551 clearly reveal two chemical relaxations. The amplitudes of these relaxation processes have identical spectral distributions, but the relaxation times show different dependences on the reactant concentrations. These findings are discussed in terms of possible models.     

Regulatory role of sphingomyelin metabolites in hypoxia-induced vascular smooth muscle cell proliferation

The rotating frame nuclear magnetic resonance relaxation rate R(1rho) in the blood and cell lysate was studied at 4.7T to provide reference values for in vivo modeling and to address the mechanisms contributing to net relaxation. A strong dependence on oxygenation, hematocrit, and spin lock field strength B(1) (0.2-1.6G) was observed in whole blood, whereas in lysate the effects were severely attenuated. The results were further compared to transverse relaxation rate R(2). A good agreement in low-field asymptotes of these two relaxation rates was found. R(1rho) field dispersion was fitted to Lorenzian line shape and resulted in correlation times around 40 micros. The dispersion behavior was related to motional properties of intracellular hemoglobin and effects of susceptibility shift interface across the cell membrane induced by compartmentalization of Hb into cells in blood.     

Influence of ionic environment of the stress relaxation behavior of an invertebrate connective tissue

The rheological properties of an invertebrate connective tissue were measured in three different ionic environments. Short-term stress relaxation tests were conducted on sections of holothurian (Echinodermata) body wall immersed in isotonic monovalent and divalent salt solutions and deionized water. Using a reduced modulus format, the viscoelastic behavior over the experimental time scale was described by a two term Maxwell equation with empirically determined spring constants and relaxation times. In addition, equilibrium relaxation moduli (Ge) were estimated from the empirical relationship of Chasset and Thirion (1965, in Physics of Non Crystalline Solids, ed. Prins, North Holland). The experiments indicated that both relaxation times and equilibrium moduli decreased in the presence of monovalent and divalent inorganic ions whereby the effect of the Na+ was greater than that of the Ca++. The present findings are compared with those reported for vertebrate connective tissue.     

Self-association of oxyhaemoglobin. A nuclear magnetic relaxation study in H2O/D2O solutions

The proton and deuterium longitudinal relaxation rates were Studied at room temperature up to the highest protein concentrations in oxyhaemoglobin solutions of different H₂O/D₂O composition. The deuterium relaxation rates followed the experimentally well known single linear dependence on protein concentration, the slopes being little influenced by solvent (D₂O/H₂O) composition. The proton ralaxation rates show two different liner dependences on haemoglobin concentration. The entire concentration range is described by two straight lines with the threshold concentration about 11 mM (in haem), The ratio of the slopes is 1.6 (high-to-low Hb-conc.). Only in the higher concentration range two T₁'s were observed if the solvent contained more than half of D₂O. The slow relaxation phase of protons has T₁'s similar to those measured in solutions with less than half of D₂O. The relaxation of the other phase was ten times faster. The ratio of the proton populations in these two phases was equal to 2 (slow-to-fast) and independent of protein concentration. The fast relaxing protons are attributed to water molecules encaged within two or more haemoglobin molecules which associate for times long enough on the PMR time-scale.     

Natural polymers according to NMR data: cross-relaxation in hydrated collagen macromolecules from two connective tissues

Spin-lattice relaxation and cross-relaxation in oriented and randomly oriented collagen fibers from two connective tissues (15-month-old calf and 8-year-old steer) at a water content of 0.6 g H2O/g dry matter were studied. Collagens were chosen according to different numbers of covalent nonreducible cross-links, which increase during the life of the animal. The spin-lattice relaxation curves for all the collagens after a 180 degree-tau-90 degree pulse sequence were described by two exponential components. The dependences of two components of spin lattice relaxation time and their populations on the length of the 180 degree-pulse were obtained. On the basis of data of Goldman-Shen sequence and the two-phase model, the populations of proton fractions (p(w) and p(c)) as well as the rates of transfer of magnetization between water protons and collagen protons (k(w) and k(c)) were calculated. No significant difference between k(w) (k(c)) in oriented and randomly oriented fibers as well as in fibers with different cross-linking was found. The estimates of the cross-relaxation times for low cross-link collagen and high cross-link one were done. The correlation times of dipole-dipole interactions for both connective tissues were calculated using the cross-relaxation theory.     

Orientation of DNA molecules in agarose gels by pulsed electric fields

The electric birefringence of DNA restriction fragments of three different sizes, 622, 1426, and 2936 base pairs, imbedded in agarose gels of different concentrations, was measured. The birefringence relaxation times observed in the gels are equal to the values observed in free solution, if the median pore diameter of the gel is larger than the effective hydrodynamic length of the DNA molecule in solution. However, if the median pore diameter is smaller than the apparent hydrodynamic length, the birefringence relaxation times increase markedly, becoming equal to the values expected for the birefringence relaxation of fully stretched DNA molecules. This apparent elongation indicates that end-on migration, or reptation is a likely mechanism for the electrophoresis of large DNA molecules in agarose gels. The relaxation times of the stretched DNA molecules scale with molecular weight (or contour length) as N2.8, in reasonable agreement with reptation theories.     

Nuclear magnetic resonance multiwindow analysis of proton local fields and magnetization distribution in natural and deuterated mouse muscle.

The proton free-induction decays, spin-spin relaxation times, local fields in the rotating frame, and spin-lattice relaxation times in the laboratory and rotating frames, in natural and fully deuterated mouse muscle, are reported. Measurements were taken above and below freezing temperature and at two time windows on the free-induction decay. A comparative analysis show that the magnetization fractions deduced from the different experiments are in good agreement. The main conclusion is that the resolution of the (heterogeneous) muscle nuclear magnetic resonance (NMR) response is improved by the multiwindow analysis.     

1H NMR Relaxometry in Natural Humous Soil Samples: Insights in Microbial Effects on Relaxation Time Distributions

¹H NMR relaxometry is applied for the investigation of pore size distributions in geological substrates. The transfer to humous soil samples requires the knowledge of the interplay between soil organic matter, microorganisms and proton relaxation. The goal of this contribution is to give first insights in microbial effects in the ¹H NMR relaxation time distribution in the course of hydration of humous soil samples. We observed the development of the transverse relaxation time distribution of the water protons after addition of water to air dried soil samples. Selected samples were treated with cellobiose to enhance microbial activity. Besides the relaxation time distribution, the respiratory activity and the total cell counts were determined as function of hydration time. Microbial respiratory activities were 2–15 times higher in the treated samples and total cell counts increased in all samples from 1×10⁹ to 5×10⁹ cells g⁻¹ during hydration. The results of ¹H NMR relaxometry showed tri-, bi- and mono-modal relaxation time distributions and shifts of peak relaxation times towards lower relaxation times of all investigated soil samples during hydration. Furthermore, we found lower relaxation times and merging of peaks in soil samples with higher microbial activity. Dissolution and hydration of cellobiose had no detectable effect on the relaxation time distributions during hydration. We attribute the observed shifts in relaxation time distributions to changes in pore size distribution and changes in spin relaxation mechanisms due to dissolution of organic and inorganic substances (e.g. Fe³⁺, Mn²⁺), swelling of soil organic matter (SOM), production and release of extracellular polymeric substances (EPS) and bacterial association within biofilms.     

The efficacy of paramagnetic ions on spin lattice relaxation time in biological systems

This paper summarizes the observations of different studies concerning the influence of paramagnetic ions on spin-lattice relaxation times. Neither the comparison between different organs, different animals nor the comparison between different tissues (normal and malignant) showed correlation of practical consequences between the paramagnetic ion concentrations in whole tissues and spin-lattice relaxation times.