CiteULike: Tag relaxation

Transverse relaxation of cells labeled with magnetic nanoparticles

CH Ziener — 2007-04-04T16:06:56-00:00

Magnetic Resonance in Medicine, Vol. 54, No. 3. (2005), pp. 702-706.

We describe the NMR relaxation properties of magnetically labeled cells. The cells are labeled with magnetic nanoparticles (SPIO, USPIO), which generate susceptibility contrast. The geometry of the labeled cells and the surrounding tissue is considered. We assume that the magnetic nanoparticles accumulate to form a magnetic core of radius RC inside the cell. The correlation time ?, which describes the motion of spins around this core, is analyzed. Using the strong collision approach, explicit expressions are derived for the transverse relaxation rate R2* for tissue containing labeled cells as a function of the core radius, the diffusion coefficient, and the concentration of the nanoparticles. The predictions of this model agree well with numerical simulations and experimental data. Magn Reson Med, 2005. © 2005 Wiley-Liss, Inc.

Implementing Constraint Relaxation over Finite Domains using ATMS

Narendra Jussien — 2007-03-29T15:35:12-00:00

No. 1106. (1996), pp. 265-280.

Many real-life Constraint Satisfaction Problems are over-constrained. In order to provide some kind of solution for such problems, this paper proposes a constraint relaxation mechanism fully integrated with the constraint solver. Such a constraint relaxation system must be able to perform two fundamental tasks: identification of constraints to relax and efficient constraint suppression. Assumption-based Truth Maintenance Systems propose a uniform framework to tackle those requirements. The main ...

Regional brain chemical alterations in young children with autism spectrum disorder.

SD Friedman — 2005-09-30T01:51:49-00:00

Neurology, Vol. 60, No. 1. (14 January 2003), pp. 100-107.

OBJECTIVE: The authors evaluated regional brain chemistry for evidence of increased neuronal packing density in autism. METHODS: Forty-five 3- to 4-year-old children with autism spectrum disorder (ASD), 13 children with typical development (TD), and 15 children with delayed development (DD) were studied using dual-echo proton echoplanar spectroscopic imaging (32 x 32 matrix-1 cm(3) voxels) to measure brain chemical concentrations and relaxation times. Chemical quantification was corrected for tissue partial volume and relative measures of chemical relaxation (T(2r)) were calculated from the paired echoes. Measures from averaged and individual regions were compared using analysis of variance corrected for multiple comparisons. RESULTS: ASD subjects demonstrated reduced N-acetylaspartate (NAA) (-10%), creatine (Cre) (-8%), and myo-inositol (-13%) concentrations compared to TD controls and prolonged NAA T(2r) relative to TD (7%) and DD (9%) groups. Compared to DD subjects, children with ASD also demonstrated prolonged T(2r) for choline (10%) and Cre (9%). Regional analyses demonstrated subtle patterns of chemical alterations in ASD compared to the TD and DD groups. CONCLUSIONS: Brain chemical abnormalities are present in ASD at 3 to 4 years of age. However, the direction and widespread distribution of these abnormalities do not support hypothesis of diffuse increased neuronal packing density in ASD.

Perceived and physiological indicators of relaxation: as different as Mozart and Alice in chains.

J Burns — 2005-11-04T08:51:28-00:00

Appl Psychophysiol Biofeedback, Vol. 24, No. 3. (September 1999), pp. 197-202.

The effects of listening to different types of music on perceived and physiological indicators of relaxation were evaluated. Fifty-six undergraduate students, 24 males and 32 females, mean age of 21, were randomly assigned to listen to classical, hard rock, self-selected relaxing music, or no music. Participants' relaxation level, skin temperature, muscle tension and heart rate were evaluated before and after exposure to a music condition. Analyses of variance using baseline measures as covariates indicated that skin temperature decreased for all conditions (p = 0.001) and the classical, self-selected relaxing music and no music groups reported significant increases in feelings of relaxation (p = 0.004). These results partially support the hypothesis that classical and self-selected relaxing music can increase perceptions of relaxation to a greater degree than listening to hard rock music. However, no differences were found between different types of music on physiological indicators of arousal. Implications for using music to reduce stress were discussed.

Direct measurement of dipole-dipole/CSA cross-correlated relaxation by a constant-time experiment

Yizhou Liu — 2008-06-02T17:22:42-00:00

Journal of Magnetic Resonance, Vol. In Press, Corrected Proof

Relaxation rates in NMR are usually measured by intensity modulation as a function of a relaxation delay during which the relaxation mechanism of interest is effective. Other mechanisms are often suppressed during the relaxation delay by pulse sequences which eliminate their effects, or cancel their effects when two data sets with appropriate combinations of relaxation rate effects are added. Cross-correlated relaxation (CCR) involving dipole-dipole and CSA interactions differ from auto-correlated relaxation (ACR) in that the signs of contributions can be changed by inverting the state of one spin involved in the dipole-dipole interaction. This property has been exploited previously using CPMG sequences to refocus CCR while ACR evolves. Here we report a new pulse scheme that instead eliminates intensity modulation by ACR and thus allows direct measurement of CCR. The sequence uses a constant time relaxation period for which the contribution of ACR does not change. An inversion pulse is applied at various points in the sequence to effect a decay that depends on CCR only. A 2-D experiment is also described in which chemical shift evolution in the indirect dimension can share the same constant period. This improves sensitivity by avoiding the addition of a separate indirect dimension acquisition time. We illustrate the measurement of residue specific CCR rates on the non-myristoylated yeast ARF1 protein and compare the results to those obtained following the conventional method of measuring the decay rates of the slow and fast-relaxing 15N doublets. The performances of the two methods are also quantitatively evaluated by simulation. The analysis shows that the shared constant-time CCR (SCT-CCR) method significantly improves sensitivity.

The effects of guided imagery on anxiety levels and movement of clients undergoing magnetic resonance imaging.

MB Thompson — 2005-07-28T17:51:24-00:00

Holist Nurs Pract, Vol. 8, No. 2. (January 1994), pp. 59-69.

This randomized, experimental study examined the effects of guided imagery on anxiety levels and on movement of clients undergoing nonemergency magnetic resonance imaging (MRI). Subjects who listened to a guided imagery/relaxation tape (n = 20) before their MRI scan and used guided imagery during their scan had lower levels of state anxiety than the control group (n = 21). Based on subject report and operator report, the experimental group moved less frequently during the MRI than the control group. The results of this investigation support the use of guided imagery as a therapeutic intervention and Rogers' Science of Unitary Human Beings.

Evaluation of three psychologic interventions to reduce anxiety during MR imaging.

ME Quirk — 2005-07-20T20:23:02-00:00

Radiology, Vol. 173, No. 3. (December 1989), pp. 759-762.

The authors compared the effectiveness of three anxiety-reducing interventions for patients undergoing magnetic resonance imaging. Each of 50 subjects was randomly assigned to one of the interventions. Intervention 1 involved provision of information about the imager and nature of the examination. Intervention 2 included information and counseling. Intervention 3 included information and a 12-minute relaxation exercise. Anxiety levels were measured by means of a 20-item questionnaire before and after imaging. The latter provided a retrospective report of anxiety experienced during imaging. Patients in intervention group 3 showed significantly less increase in anxiety compared with those in groups 1 and 2. Overall, only patients who participated in intervention 1 showed a significant increase in anxiety during imaging. When anxiety levels experienced before and during the examination were compared, with the focus on each questionnaire item for each group, those in group 1 showed a significant increase in anxiety on eight of 20 items; those in group 2, three items; and those in group 3, none. Psychologic preparation that includes relaxation strategies is more effective than provision of information alone.

Helping children relax during magnetic resonance imaging.

G Smart — 2005-07-19T21:00:33-00:00

MCN Am J Matern Child Nurs, Vol. 22, No. 5. (t 1997), pp. 236-241.

Every day, pediatric nurses face the challenge of comforting hospitalized children, managing their pain, and supporting their parents. While pharmacologic therapy remains the first-line strategy for pain management, a wide variety of nonpharmacologic techniques are also available for enchancing comfort. (See "Cognitive and behavioral strategies to reduce children's pain," by Mary K. Kachoyeanos and margaret Friedhoff, MCN, 18:14-19, Jan.-Feb.1993.) Nurses can easily teach children and parents to use these modalities, both to reduce pain and to allay any anxiety they may have.

Detection and location of moving objects using deterministic relaxation algorithms

Nikos Paragios — 2006-08-31T10:42:53-00:00

No. TR95-0155. (1995)

Two important problems in motion analysis are addressed in this paper: change detection and moving object location. For the first problem, the inter-frame difference is modelized by a mixture of Laplacian distributions, a Gibbs random field is used for describing the label field, and ICM (Iterated Conditional Modes) or HCF (Highest Confidence First) algorithms are used for solving the resulting optimization problem. The solution of the second problem is based on the observation of two...

The Individualistic Dynamics of Entangled DNA in Solution

RE Teixeira — 2007-05-22T09:19:11-00:00

Macromolecules, Vol. 40, No. 7. (3 April 2007), pp. 2461-2476.

Abstract: We present the direct visualizations of single, entangled DNA polymers in three flow experiments: relaxation following a rapid shear deformation, steady shear, and startup shear. To evaluate molecular theories, "test" chains were stained against a background of unstained but otherwise identical chains. To provide a direct link to bulk viscoelasticity, identical preparations were also extensively characterized via mechanical rheometry. The four concentrations studied displayed similar rheological features to synthetic polymers at comparable concentrations and were accordingly classified from semidilute to well-entangled. In entangled solutions, we uncovered two distinct relaxation time scales, with the fast, chain retraction characteristic time, fast 10-fold longer than the rotational Rouse time assumed by theoretical models. We also found a high degree of molecular individualism and broad conformational distributions in all experiments at shear rates > . This new evidence restricts the applicability of the pre-averaging approximation underlying all closed-form theories developed to date and explains some of the complications in modeling nonlinear flows.

Evaluation methods of the longest Rouse relaxation time of an entangled polymer in a semidilute solution

K Osaki — 2006-10-10T08:43:07-00:00

Journal of Polymer Science Part B: Polymer Physics, Vol. 39, No. 14. (2001), pp. 1704-1712.

Estimation methods for the longest Rouse relaxation time (?R) of an entangled polymer in a semidilute solution were examined. We evaluated ?R by fitting the dynamic modulus (G?) with the Rouse model theory in the power law range, where G? was proportional to the square root of the angular frequency (?). The ?R values thus obtained for polystyrene (PS) solutions in tricresyl phosphate (TCP) were employed to derive an empirical formula for the evaluation of ?R from the viscosity (?): M is the molecular weight, and c is the mass of polymer per unit volume; Me = cRT/GN is the entanglement molecular weight, where GN is the G? value at the inflection point of the graph of log G? versus log ?. The subscript ? indicates that ?R is derived from ? data. The proposed equation was also applicable to bulk PS and bulk polyisoprene. Discrepancies among reported ?R values in semidilute solutions seem to be mostly due to discrepancies in Me values. For PS solutions in dioctyl phthalate, a ? solvent, the ?R value derived from ? was much larger than that from the G? curve. Apart from the evaluation method of ?R, we observed for PS that Me was independent of temperature for good solvent systems and melts, that Me for solutions in TCP agreed with that for solutions in another good solvent, and that Me for a ?-solvent system was equal to that for good solvent systems with the same M and c values. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 1704-1712, 2001

Segment connectivity, chain-length breathing, segmental stretch, and constraint release in reptation models. I. Theory and single-step strain predictions

Chi Hua — 2006-08-04T17:41:48-00:00

The Journal of Chemical Physics, Vol. 109, No. 22. (1998), pp. 10018-10027.

A self-consistent reptation theory that accounts for chain-tube interactions, segment connectivity, chain-length breathing, segmental stretch, and constraint release is proposed. Simulation results are compared semiquantitatively to experimental observations in single-step strain flows. Since stochastic simulation techniques are used, no approximations, such as independent alignment or consistent averaging are needed to obtain results. The simulation results show excellent agreement with experimental trends in shear and normal stress relaxations, including the second normal stress difference, well into the nonlinear regime. For most of these experiments, the original Doi and Edwards theory, which incorporates independent alignment or consistent averaging, is not satisfactory. In the following companion paper, we show how the model is capable of describing double-step-strain flows for all stress components. Subsequent papers show excellent agreement for the inception of steady shear flow, and steady shear flow. ©1998 American Institute of Physics.

Hierarchies and Logarithmic Oscillations in the Temporal Relaxation Patterns of Proteins and other Complex Systems

R Metzler — 2007-04-04T12:53:37-00:00

Proceedings of the National Academy of Science, Vol. 96 (September 1999), pp. 11085-11089.

Logarithmic oscillations superimposed on the temporal relaxation patterns of complex systems are considered from the standpoint of their hierarchical origin. We propose that a closer examination of experimental data should reveal logarithmic oscillations in systems that are characterized by a hierarchical structure of their dynamical degrees of freedom. On that footing, a new methodology of data analysis is proposed that may prove important for the dynamics of protein folding and of conformational fluctuations in proteins in which the relevant time scales of the dynamical evolution underlying the relaxation kinetics can be deduced from these oscillations.<p>

Semiclassical kinetic theory of electron spin relaxation in semiconductors

Franz Bronold — 2007-05-07T09:11:11-00:00

Physical Review B (Condensed Matter and Materials Physics), Vol. 70, No. 24. (2004)

We develop a semiclassical kinetic theory for electron spin relaxation in semiconductors. Our approach accounts for elastic as well as inelastic scattering and treats Elliott-Yafet and motional-narrowing processes, such as D'yakonov-Perel' and variable g-factor processes, on an equal footing. Focusing on small spin polarizations and small momentum transfer scattering, we derive, starting from the full quantum kinetic equations, a Fokker-Planck equation for the electron spin polarization. We then construct, using a rigorous multiple time scale approach, a Bloch equation for the macroscopic (-averaged) spin polarization on the long time scale, where the spin polarization decays. Spin-conserving energy relaxation and diffusion, which occur on a fast time scale, after the initial spin polarization has been injected, are incorporated and shown to give rise to a weight function that defines the energy averages required for the calculation of the spin relaxation tensor in the Bloch equation. Our approach provides an intuitive way to conceptualize the dynamics of the spin polarization in terms of a "test" spin polarization that scatters off "field" particles (electrons, impurities, phonons). To illustrate our approach, we calculate for a quantum well the spin lifetime at temperatures and densities where electron-electron and electron-impurity scattering dominate. The spin lifetimes are nonmonotonic functions of temperature and density. Our results show that at electron densities and temperatures where the crossover from the nondegenerate to the degenerate regime occurs, spin lifetimes are particularly long.

Relaxation Dynamics of Entangled and Unentangled Multiarm Polymer Solutions: Experiment

Juliani — 2007-12-19T16:59:58-00:00

Macromolecules, Vol. 35, No. 18. (27 August 2002), pp. 6953-6960.

Abstract: Relaxation dynamics of several model A3-A-A3 multiarm 1,4-polybutadiene melts and solutions are investigated experimentally using small amplitude oscillatory shear rheometry over a broad temperature range (-90 to +26 C). Two rubbery plateaus are identified from loss G' '() minima at low frequencies. The storage modulus in the first plateau regime is of similar magnitude to the plateau modulus GN0 of entangled linear 1,4-polybutadiene melts, and varies with multiarm solution concentration pom as GN(pom) = GN0. The second low-frequency plateau modulus GN,II increases with crossbar A volume fraction cb in nearly the manner expected for dynamics of crossbar segments in a network diluted by relaxed arms, A (i.e., GN,II GN(pom)cb1+, with 1.3). Despite this, we find that arms exert a profound influence on crossbar dynamics well after they have relaxed. Specifically, at solution concentrations helow the threshold for arm entanglement, the zero-shear viscosity of multiarm solutions vary with pom as 0 ~ pom2.9±0.2, which is slightly weaker than expected for entangled linear polymers without contour length fluctuations. However, for these same materials the terminal time is found to depend more strongly than expected on solution concentration, ~ pom2.6±0.3. At polymer concentrations above the threshold for arm entanglements, a transition to much stronger terminal property scalings with solution concentration and molecular weight are observed. In particular, for arm entanglement densities above two, the zero-shear viscosity and terminal time of multiarm solutions are exponential functions of overall polymer molecular weight and concentration.

Determination of discrete relaxation spectra using Simulated Annealing

Erik Jensen — 2007-08-07T14:28:57-00:00

Journal of Non-Newtonian Fluid Mechanics, Vol. 107, No. 1-3. (6 December 2002), pp. 1-11.

Simulated Annealing (SA), a Monte Carlo method, is used to obtain discrete relaxation spectra from small strain oscillatory shear measurements. The SA algorithm does so by evaluating randomly generated trial values of relaxation moduli, gk, and relaxation times, [lambda]k. If the solution of a trial point gives a lower function value, it is accepted as a new minimum. The solution can escape from local minima by using the Metropolis criterion which accepts an uphill move during minimisation given a certain probability. SA searches for the global optima, i.e. the best fit. In order to avoid fitting of noise, only a limited number of modes are fitted. Constraints can easily be imposed on the solution to ensure that the relaxation times are kept within the limits of sampling localisation and to avoid the calculation of negative gk and [lambda]k. The results demonstrate SA's ability to fit a relaxation spectrum with a short computation time. The quality of the fit is determined by the truncated data range, and, to a certain degree, by a chosen sampling localisation limit.

Systematic Review of Relaxation Interventions for Pain

Kwekkeboom — 2006-08-19T09:19:43-00:00

Journal of Nursing Scholarship, Vol. 38, No. 3. (September 2006), pp. 269-277.

Microsecond-to-Millisecond Conformational Dynamics Demarcate the GluR2 Glutamate Receptor Bound to Agonists Glutamate, Quisqualate, and AMPA

ER Valentine — 2008-03-21T21:39:05-00:00

Biochemistry, Vol. 44, No. 9. (8 March 2005), pp. 3410-3417.

Abstract: Chemical shift changes and internal motions on microsecond-to-millisecond time scales of the S1S2 ligand-binding domain of the GluR2 ionotropic glutamate receptor have been studied by NMR spectroscopy in the presence of the agonists glutamic acid (glutamate), quisqualic acid (quisqualate), and -amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA). Although the crystal structures of the three agonist-bound forms of GluR2 S1S2 ligand-binding domain are very similar, chemical shift changes imply that AMPA-bound GluR2 S1S2 is conformationally distinct from glutamate- and quisqualate-bound forms of GluR2 S1S2. NMR spin relaxation measurements for backbone amide 15N nuclei reveal that GluR2 S1S2 exhibits reduced chemical exchange line broadening, resulting from microsecond-to-millisecond conformational dynamics, in AMPA-bound compared to glutamate- and quisqualate-bound states. The largest changes in line broadening are observed for two regions of GluR2 S1S2: Val683 and the segment around Lys716-Cys718. The differences in binding affinity of these agonists do not explain the differences in microsecond-to-millisecond conformational dynamics because quisqualate and AMPA bind with similar affinities that are 10-fold greater than the affinity of glutamate. Differences in conformational mobility may reflect differences in the binding mode of AMPA in the GluR2 S1S2 active site compared to the other two ligands. The sites of conformational mobility in GluR2 S1S2 imply that subtle differences exist between the agonists glutamate, quisqualate, and AMPA in modulating glutamate receptor function.

On the measurement of 15N-1H nuclear Overhauser effects

Fabien Ferrage — 2008-06-02T17:29:40-00:00

Journal of Magnetic Resonance, Vol. 192, No. 2. (June 2008), pp. 302-313.

Accurate quantification of the 15N-1H steady-state NOE is central to current methods for the elucidation of protein backbone dynamics on the fast, sub-nanosecond time scale. This experiment is highly susceptible to systematic errors arising from multiple sources. The nature of these errors and their effects on the determined NOE ratio is evaluated by a detailed analysis of the spin dynamics during the pair of experiments used to measure this ratio and possible improvements suggested. The experiment that includes 1H irradiation, is analyzed in the framework of Average Liouvillian Theory and a modified saturation scheme that generates a stable steady-state and eliminates the need to completely saturate 1H nuclei is presented. The largest source of error, however, in 1H-dilute systems at ultra-high fields is found to be an overestimation of the steady-state NOE value as a consequence of the incomplete equilibration of the magnetization in the so-called "reference experiment". The use of very long relaxation delays is usually an effective, but time consuming, solution. Here, we introduce an alternative reference experiment, designed for larger, deuterated systems, that uses the fastest relaxing component of the longitudinal magnetization as a closer approximation to the equilibrium state for shorter relaxation delays. The utility of the modified approach is illustrated through simulations on realistic spin systems over a wide range of time scales and experimentally verified using a perdeuterated sample of human ubiquitin.

NMR characterization of the dynamics of biomacromolecules.

AG Palmer — 2008-06-19T17:13:02-00:00

Chemical reviews, Vol. 104, No. 8. (August 2004), pp. 3623-3640.

Dynamics of the phosphate group in phospholipid bilayers. A 31P-1H transient Overhauser effect study.

MP Milburn — 2008-05-15T23:52:23-00:00

Biophys. J., Vol. 58, No. 1. (1 July 1990), pp. 187-194.

Two recent studies have addressed the question of the dynamics of the phosphate in egg phosphatidylcholine multilayers by measurement and interpretation of 31P NMR spin-lattice relaxation. In the first (Milburn, M. P., and K. R. Jeffrey. 1987. Biophys. J. 52:791-799), the temperature dependences of the two contributions to the 31P relaxation rate, a dipolar interaction of the phosphorus with neighboring protons and a time-dependent anisotropic chemical shielding interaction were separately measured. A further study (Milburn, M. P., and K. R. Jeffrey. 1989. Biophys. J. 56:543-549) incorporated the anisotropic nature of phospholipid motions into the dynamic model of the headgroup motion by measuring the 31P spin-lattice relaxation time in oriented samples as a function of angle between the bilayer normal and the magnetic field. These angular dependent measurements were made at high field so that analysis could by made using the chemical shielding interaction because the 31P-1H dipolar interaction in phospholipid systems is complex and as such poorly understood. Nuclear Overhauser effect (NOE) studies have attempted to identify the important proton species contributing to the 31P-1H dipolar interaction (Yeagle, P. L., W. C. Hutton, C. Huang, and R. B. Martin. 1975. Biochemistry. 15:2121-2124) and despite some controversy in interpretation (Burns, R. A., R. E. Stark, D. A. Vidusek, and M. F. Roberts. 1983. Biochemistry. 22:5084-5090), it was generally agreed that the choline methyl and methylene protons are the major contributors to the 31P-1H NOE. To further understand the nature of the 31P-1H dipolar interaction, we carried out 31P-1H Transient Overhauser effect (TOE) measurements on egg phosphatidylcholine multilayers.(ABSTRACT TRUNCATED AT 250 WORDS)

Dynamics of the phosphate group in phospholipid bilayers. A 31P angular dependent nuclear spin relaxation time study.

MP Milburn — 2008-05-30T00:15:00-00:00

Biophys. J., Vol. 56, No. 3. (1 September 1989), pp. 543-549.

To understand 31P relaxation processes and hence molecular dynamics in the phospholipid multilayer it is important to measure the dependence of the 31P spin-lattice relaxation time on as many variables as the physical system allows. Such measurements of the 31P spin-lattice relaxation rate have been reported both as a function of Larmor frequency and temperature for egg phosphatidylcholine liposomes (Milburn, M.P., and K.R. Jeffrey. 1987. Biophys. J. 52:791-799). In principle, the spin-lattice relaxation rate in an anisotropic environment such as a bilayer will be a function of the angle between the bilayer normal and the magnetic field. However, the measurement of this angular dependence has not been possible because the rapid (on the time-scale of the spin-lattice relaxation rate) diffusion of the lipid molecules over the curved surface of the liposome average this dependence (Milburn, M.P., and K.R. Jeffrey. 1987. Biophys. J. 52:791-799; Brown, M.F., and J.H. Davis. 1981. Chem. Phys. Lett. 79:431-435). This paper reports the results of the measurement of the 31P spin-lattice relaxation rate as a function of this angle, beta', (the angle between the bilayer normal and the external magnetic field) using samples oriented between glass plates. These measurements were made at high field (145.7 MHz) where the spin-lattice relaxation processes are dominated by the chemical shielding interaction (Milburn, M.P., and K.R. Jeffrey. 1987. Biophys. J. 52:791-799). A model of molecular motion that includes a fast axially symmetric rotation of the phosphate group (tau i approximately 10(-9) s) and a wobble of the head group tilt with respect to this rotation axis has been used to describe both the angular dependence of the spin-lattice relaxation and the spectral anisotropy.(ABSTRACT TRUNCATED AT 250 WORDS)

Transition from Micelles to Vesicles in Aqueous Mixtures of Anionic and Cationic Surfactants

O Soderman — 2008-05-10T07:00:55-00:00

Langmuir, Vol. 13, No. 21. (15 October 1997), pp. 5531-5538.

Abstract: Vesicles form spontaneously in a variety of aqueous mixtures of oppositely charged surfactants. Here we report the morphological transition from spherical micelles to vesicles observed in mixtures of dodecyltrimethylammonium chloride (DTAC) and sodium dodecylbenzenesulfonate (SDBS) as probed by the complementary techniques of quasielastic light scattering (QLS), NMR self-diffusion and relaxation measurements, and time-resolved fluorescence quenching (TRFQ) experiments. In these mixtures, there is limited growth of the micelles with changes in composition, and vesicles abruptly begin to form at a characteristic mixing ratio of the two surfactants. As the composition moves further into the vesicle region, the quantity of micelles decreases in proportion to the number of vesicles that form. Thus, in mixtures of DTAC and SDBS, the transition from micelles to vesicles is continuous. This is in contrast to the first-order phase transition exhibited by other aqueous mixtures of oppositely charged surfactants, in which micelles first grow into extended threadlike micelles and samples intermediate to the micellar and vesicle phases separate into two macroscopic phases.

31P NMR relaxation studies of the activation of the coenzyme phosphate of glycogen phosphorylase. The role of motion of the bound phosphate.

SG Withers — 2008-05-30T00:04:12-00:00

Biophysical journal, Vol. 48, No. 6. (December 1985), pp. 1019-1026.

Spin-lattice and spin-spin relaxation rates (1/T1 and 1/T2) have been determined for the catalytically essential coenzyme phosphate at the active site of glycogen phosphorylase in both activated (R state) and inactive (T state) conformations of the enzyme. Dipolar contributions to 31P relaxation due to exchangeable protons on the phosphate group have been determined by measurement of relaxation rates at different concentrations of H2O and D2O, and field dependence studies have been performed to estimate the contribution of chemical shift anisotropy to the remaining 31P relaxation in D2O. At 109 MHz, dipolar relaxation from exchangeable protons was found to account for 50% of the spin-lattice relaxation for activated phosphorylase in 75% H2O, the remainder being due to chemical shift anisotropy. The spin-lattice relaxation rates in D2O for R-state glycogen phosphorylase are very similar to those measured for other proteins of very different size such as actin (Brauer, M., and B. D. Sykes, 1981, Biochemistry. 20:6767-6775), alkaline phosphatase (Coleman, J. E., I. D. Armitage, J. F. Chlebowski, J. D. Otvos, and A. J. M. S. Uiterkamp, 1979), and phosphoglucomutase (Rhyu, G. I., W. J. Ray, Jr., and J. L. Markley, 1984, Biochemistry. 23:252-260). In inactive (T state) phosphorylase the spin-lattice relaxation rates were almost an order of magnitude slower, while the spin-spin relaxation rates were essentially identical. These results have been analyzed by calculating the theoretically expected 31P relaxation rates in the presence of internal motions that are included in the relaxation calculation using the model-free approach of Lipari and Szabo (1982, J. Am. Chem. Soc. 104:4564-4559).(ABSTRACT TRUNCATED AT 250 WORDS)

Research on the Vesicle-Micelle Transition by 1H NMR Relaxation Measurement

M Villeneuve — 2008-05-10T06:49:41-00:00

J. Phys. Chem. B, Vol. 110, No. 36. (14 September 2006), pp. 17830-17839.

Abstract: We have investigated how the dynamics of surfactant molecules changes with the vesicle-micelle transition by 1H NMR relaxation studies on the sodium decyl sulfate (SDeS)-decyltrimethylammonium bromide (DeTAB)-deuterium oxide system. The study has been planned with reference to the phase diagram of the SDeS-DeTAB-water system deduced from thermodynamic analysis of the surface tension data. The spin-lattice relaxation time (T1) and the spin-spin relaxation time (T2) are measured at 90 and 400 MHz at various total molalities, m, and compositions, X2, of the surfactants. The data were analyzed according to the "two-step" model developed by Wennerström et al. and molecular dynamics of the surfactant is discussed from the viewpoint of correlation time f associated with the local fast motion of the surfactant molecule, correlation time s associated with the slow overall motions of the aggregate and surfactant molecules within it, and local order parameter S. We find s of vesicles is an order of magnitude larger than that of micelles signifying that the tumbling of vesicle particles and surfactant diffusion over the vesicle are much slower than those for micelle. f and S for vesicles are also larger than those for micelles. Molecular environments of the surfactant are also discussed from the dependence of the chemical shifts on m at constant X2 or from that on X2 at constant m. When the chemical shifts in vesicle and micelle are compared at constant m, the chemical shifts in vesicle are displaced to a lower magnetic field than those in micelle, which implies that the surfactant molecules are arranged more closely to each other in the vesicle than in the micelle.

Quantitative NMR spectroscopy of supramolecular complexes: Dynamic side pores in ClpP are important for product release

Remco Sprangers — 2008-06-19T16:58:28-00:00

Proceedings of the National Academy of Sciences, Vol. 102, No. 46. (15 November 2005), pp. 16678-16683.

The highly conserved, 300-kDa cylindrical protease ClpP is an important component of the cellular protein quality machinery. It consists of 14 subunits arranged into two heptameric rings that enclose a large chamber containing the protease active sites. ClpP associates with ClpX and ClpA ATPases that unfold and translocate substrates into the protease catalytic chamber through axial pores located at both ends of the ClpP cylinder. Although the pathway of substrate delivery is well established, the pathway of product release is unknown. Here, we use recently developed transverse relaxation optimized spectroscopy (TROSY) of methyl groups to show that the interface between the heptameric rings exchanges between two structurally distinct conformations. The conformational exchange process has been quantified by magnetization exchange and methyl TROSY relaxation dispersion experiments recorded between 0.5degreesC and 40degreesC, so that the thermodynamic properties for the transition could be obtained. Restriction of the observed motional freedom in ClpP through the introduction of a cysteine linkage results in a protease where substrate release becomes significantly slowed relative to the rate observed in the reduced enzyme, suggesting that the observed motions lead to the formation of transient side pores that may play an important role in product release. 10.1073/pnas.0507370102

Direct 13C-detection for carbonyl relaxation studies of protein dynamics

Gabriela Pasat — 2008-06-02T17:06:47-00:00

Journal of Magnetic Resonance, Vol. In Press, Corrected Proof

We describe a method that uses direct 13C-detection for measuring rotating-frame carbonyl (13CO) relaxation rates to describe protein functional dynamics. Key advantages of method include the following: (i) unique access to 13CO groups that lack a scalar-coupled 15N-1H group; (ii) insensitivity to 15N/1H exchange-broadening that can derail 1H-detected 15N and HNCO methods; (iii) avoidance of artifacts caused by incomplete water suppression. We demonstrate the approach for both backbone and side-chain 13CO groups. Accuracy of the 13C-detected results is supported by their agreement with those obtained from established HNCO-based approaches. Critically, we show that the 13C-detection approach provides access to the 13CO groups of functionally important residues that are invisible via 1H-detected HNCO methods because of exchange-broadening. Hence, the 13C-based method fills gaps inherent in canonical 1H-detected relaxation experiments, and thus provides a novel complementary tool for NMR studies of biomolecular flexibility.

The role of protein motions in molecular recognition: insights from heteronuclear NMR relaxation measurements

Andrew — 2008-04-23T17:23:06-00:00

Progress in Nuclear Magnetic Resonance Spectroscopy, Vol. 44, No. 3-4. (30 July 2004), pp. 141-187.

Intrinsic dynamics of an enzyme underlies catalysis

Elan Eisenmesser — 2005-11-03T02:12:29-00:00

Nature, Vol. 438, No. 7064., pp. 117-121.

Hadamard NMR spectroscopy for relaxation measurements of large (>35 kDa) proteins

B Burnley — 2008-05-01T00:19:45-00:00

Journal of Biomolecular NMR, Vol. 39, No. 3. (16 November 2007), pp. 239-245.

Abstract Here we present a suite of pulse sequences for the measurement of 15N T1, T1ρ and NOE data that combine traditional TROSY-based pulse sequences with band-selective Hadamard frequency encoding. The additive nature of the Hadamard matrix produces much reduced resonance overlap without the need for an increase in the dimensionality of the experiment or a significant decrease in the signal to noise ratio. We validate the accuracy of these sequences in application to ubiquitin and demonstrate their utility for relaxation measurements in Escherichia coli Class II fructose 1,6-bisphosphate aldolase (FBP-aldolase), a 358 residue 78 kDa dimeric enzyme.

Changes in Calmodulin Main-Chain Dynamics upon Ligand Binding Revealed by Cross-Correlated NMR Relaxation Measurements

T Wang — 2008-06-23T17:41:01-00:00

J. Am. Chem. Soc., Vol. 127, No. 3. (26 January 2005), pp. 828-829.

Abstract: The fast dynamics of protein backbones are often investigated by nuclear magnetic relaxation experiments that report on the degree of spatial restriction of the amide bond vector. By comparing calmodulin in the peptide-bound and peptide-free states with these classical methods, we observe little difference in the dynamics of the polypeptide main chain (average order parameter decrease of 0.01 unit upon binding). However, when using NMR methods that monitor the mobility of the CO-C bond vector, we reveal a significant reduction of dynamics of the protein main chain (average order parameter decrease of 0.048 units). Previous investigations have suggested that the side-chain dynamics is reduced by an average of 0.07 order parameter units upon ligand binding (Lee, A. L.; Kinnear, S. A.; Wand, A. J. Nat. Struct. Biol. 2000, 7, 72-77). The current findings suggest that the change of the CO-C bond vector dynamics is intermediate between the changes in NH and side-chain dynamics and report a previously undetected loss of main-chain entropy. Weak site-to-site correlations between the different motional indicators are also observed.

Phi-Value analysis of a three-state protein folding pathway by NMR relaxation dispersion spectroscopy

Philipp Neudecker — 2007-10-24T16:12:15-00:00

Proceedings of the National Academy of Sciences, Vol. 104, No. 40. (2 October 2007), pp. 15717-15722.

Experimental studies of protein folding frequently are consistent with two-state folding kinetics. However, recent NMR relaxation dispersion studies of several fast-folding mutants of the Fyn Src homology 3 (SH3) domain have established that folding proceeds through a low-populated on-pathway intermediate, which could not be detected with stopped-flow experiments. The dispersion experiments provide precise kinetic and thermodynamic parameters that describe the folding pathway, along with a detailed site-specific structural characterization of both the intermediate and unfolded states from the NMR chemical shifts that are extracted. Here we describe NMR relaxation dispersion Phi-value analysis of the A39V/N53P/V55L Fyn SH3 domain, where the effects of suitable point mutations on the energy landscape are quantified, providing additional insight into the structure of the folding intermediate along with per-residue structural information of both rate-limiting transition states that was not available from previous studies. In addition to the advantage of delineating the full three-state folding pathway, the use of NMR relaxation dispersion as opposed to stopped-flow kinetics to quantify Phi values facilitates their interpretation because the obtained chemical shifts monitor any potential structural changes along the folding pathway that might be introduced by mutation, a significant concern in their analysis. Phi-Value analysis of several point mutations of A39V/N53P/V55L Fyn SH3 establishes that the [beta]3[beta]4-hairpin already is formed in the first transition state, whereas strand [beta]1, which forms nonnative interactions in the intermediate, does not fully adopt its native conformation until after the final transition state. The results further support the notion that on-pathway intermediates can be stabilized by nonnative contacts. 10.1073/pnas.0705097104

Semi-classical nuclear spin relaxation theory revisited for use with biological macromolecules

Peter Luginbühl — 2008-06-23T17:37:03-00:00

Progress in Nuclear Magnetic Resonance Spectroscopy, Vol. 40, No. 3. (29 April 2002), pp. 199-247.

NMR Dynamics-Derived Insights into the Binding Properties of a Peptide Interacting with an SH2 Domain

PJ Finerty — 2008-06-02T20:27:54-00:00

Biochemistry, Vol. 44, No. 2. (18 January 2005), pp. 694-703.

Abstract: The signal transduction protein phospholipase C-1 (PLC-1) is activated when its C-terminal SH2 domain (PLCC) binds the phosphorylated Tyr-1021 site (pTyr-1021) in the -platelet-derived growth factor receptor (PDGFR). To better understand the contributions that dynamics make to binding, we have used NMR relaxation experiments to investigate the motional properties of backbone amide and side chain methyl groups in a peptide derived from the pTyr-1021 site of PDGFR, both free and in complex with the PLCC SH2 domain. The free peptide has relaxation properties that are typical for a small, unstructured polymer, while the backbone of the bound peptide is least flexible for residues in the central portion of the binding site with the amplitude of pico- to nanosecond time scale motions increasing toward the C-terminus of the peptide. The increase in large amplitude motion toward the end of the pY1021 peptide is consistent with the bound peptide existing as an ensemble of states with C-terminal residues having the broadest distribution of backbone conformations, while residues in the central binding site are the most restricted. Deuterium spin relaxation experiments establish that the protein-peptide interface is highly dynamic, and this mobility may play an important role in modulating the affinity of the interaction.

Slow Exchange in the Chromophore of a Green Fluorescent Protein Variant

MHJ Seifert — 2008-06-02T20:24:34-00:00

J. Am. Chem. Soc., Vol. 124, No. 27. (10 July 2002), pp. 7932-7942.

Abstract: Green fluorescent protein and its mutants have become valuable tools in molecular biology. They also provide systems rich in photophysical and photochemical phenomena of which an understanding is important for the development of new and optimized variants of GFP. Surprisingly, not a single NMR study has been reported on GFPs until now, possibly because of their high tendency to aggregate. Here, we report the 19F nuclear magnetic resonance (NMR) studies on mutants of the green fluorescent protein (GFP) and cyan fluorescent protein (CFP) labeled with fluorinated tryptophans that enabled the detection of slow molecular motions in these proteins. The concerted use of dynamic NMR and 19F relaxation measurements, supported by temperature, concentration- and folding-dependent experiments provides direct evidence for the existence of a slow exchange process between two different conformational states of CFP. 19F NMR relaxation and line shape analysis indicate that the time scale of exchange between these states is in the range of 1.2-1.4 ms. Thermodynamic analysis revealed a difference in enthalpy H0 = (18.2 ± 3.8) kJ/mol and entropy TS0 = (19.6 ± 1.2) kJ/mol at T = 303 K for the two states involved in the exchange process, indicating an entropy-enthalpy compensation. The free energy of activation was estimated to be approximately 60 kJ/mol. Exchange between two conformations, either of the chromophore itself or more likely of the closely related histidine 148, is suggested to be the structural process underlying the conformational mobility of GFPs. The possibility to generate a series of single-atom exchanges ("atomic mutations") like H F in this study offers a useful approach for characterizing and quantifying dynamic processes in proteins by NMR.

Model-Free Approach beyond the Borders of Its Applicability

Dmitry Korzhnev — 2008-06-23T17:33:18-00:00

Journal of Magnetic Resonance, Vol. 127, No. 2. (August 1997), pp. 184-191.

Model calculations presented in this article show that commonly used methodology of15N relaxation data analysis completely fails in detecting nanosecond time scale motions if the major part of the molecule is involved in these motions. New criteria are introduced for the detection of such cases, based on the dependence of the apparent overall correlation time, derived from theT1/T2ratio, on the spectrometer frequency. Correctly estimating the overall rotation correlation time [tau]Rwas shown to play the key role in model-free data analysis. It is found, however, that in cases of slow internal motions with characteristic times of more than 3-4 ns, the effective [tau]Rprovided by theT1/T2ratio for individual amide nitrogens can be used for the characterization of the fast picosecond internal dynamics.

Sensitivity enhancement in NMR of macromolecules by application of optimal control theory

Dominique Frueh — 2008-04-04T22:02:41-00:00

Journal of Biomolecular NMR, Vol. 32, No. 1. (17 May 2005), pp. 23-30.

NMR of macromolecules is limited by large transverse relaxation rates. In practice, this results in low efficiency of coherence transfer steps in multidimensional NMR experiments, leading to poor sensitivity and long acquisition times. The efficiency of coherence transfer can be maximized by design of relaxation optimized pulse sequences using tools from optimal control theory. In this paper, we demonstrate that this approach can be adopted for studies of large biological systems, such as the 800 kDa chaperone GroEL. For this system, the 1H–15N coherence transfer module presented here yields an average sensitivity enhancement of 20–25% for cross-correlated relaxation induced polarization transfer (CRIPT) experiments.

From the Cover: Direct NMR observation of a substrate protein bound to the chaperonin GroEL

Reto Horst — 2008-06-12T02:39:06-00:00

Proceedings of the National Academy of Sciences, Vol. 102, No. 36. (6 September 2005), pp. 12748-12753.

The reaction cycle and the major structural states of the molecular chaperone GroEL and its cochaperone, GroES, are well characterized. In contrast, very little is known about the nonnative states of the substrate polypeptide acted on by the chaperonin machinery. In this study, we investigated the substrate protein human dihydrofolate reductase (hDHFR) while bound to GroEL or to a single-ring analog, SR1, by NMR spectroscopy in solution under conditions where hDHFR was efficiently recovered as a folded, enzymatically active protein from the stable complexes upon addition of ATP and GroES. By using the NMR techniques of transverse relaxation-optimized spectroscopy (TROSY), cross-correlated relaxation-induced polarization transfer (CRIPT), and cross-correlated relaxation-enhanced polarization transfer (CRINEPT), bound hDHFR could be observed directly. Measurements of the buildup of hDHFR NMR signals by different magnetization transfer mechanisms were used to characterize the dynamic properties of the NMR-observable parts of the bound substrate. The NMR data suggest that the bound state includes random coil conformations devoid of stable native-like tertiary contacts and that the bound hDHFR might best be described as a dynamic ensemble of randomly structured conformers. 10.1073/pnas.0505642102

Backbone Dynamics ofEscherichia coliRibonuclease HI: Correlations with Structure and Function in an Active Enzyme

Arthur Mandel — 2008-05-23T22:15:17-00:00

Journal of Molecular Biology, Vol. 246, No. 1. (10 February 1995), pp. 144-163.

Ribonuclease H is an endonuclease that hydrolyzes the RNA moiety of RNA-DNA duplex molecules.Escherichia coliribonuclease H is involved in DNA replication, and retroviral ribonuclease H is essential for reverse transcription of the viral genome. To characterize the intramolcular dynamical properties ofE. coliribonuclease H, spin-lattic relaxation rate constants, spin-spin relaxation rate constants and steady state nuclear Overhauser effects for the15N nuclear spins were measured by using proton-detected heteronuclear NMR spectroscopy. The relaxation data were analyzed by using a series of dynamical models in conjunction with a statistical model selection protocol. Ribonuclease H exhibits a complex array of dynamical features, most notably in the parallel [beta]-strands of the principal five-stranded [beta]-sheet, the coiled-coil helical interface, the active site, and the loop regions surrounding the active site. The dynamical properties are correlated with local structural environments of the15N spins and suggest possible relationships to the functional properties of ribonuclease H. Results forE. coliribonuclease H are compared to previously reported results for the human immunodeficiancy virus type 1 ribonuclease H domain of reverse transcriptase.

Off-resonance rotating-frame amide proton spin relaxation experiments measuring microsecond chemical exchange in proteins

Patrik Lundstrom — 2005-07-26T16:15:42-00:00

Journal of Biomolecular NMR, Vol. 32, No. 2. (June 2005), pp. 163-173.

Polarization transfer by cross-correlated relaxation in solution NMR with very large molecules

Roland Riek — 2008-06-12T02:33:42-00:00

Proceedings of the National Academy of Sciences, Vol. 96, No. 9. (27 April 1999), pp. 4918-4923.

10.1073/pnas.96.9.4918

A solution NMR study showing that active site ligands and nucleotides directly perturb the allosteric equilibrium in aspartate transcarbamoylase

Algirdas Velyvis — 2008-05-23T22:08:53-00:00

Proceedings of the National Academy of Sciences, Vol. 104, No. 21. (22 May 2007), pp. 8815-8820.

The 306-kDa aspartate transcarbamoylase is a well studied regulatory enzyme, and it has emerged as a paradigm for understanding allostery and cooperative binding processes. Although there is a consensus that the cooperative binding of active site ligands follows the Monod-Wyman-Changeux (MWC) model of allostery, there is some debate about the binding of effectors such as ATP and CTP and how they influence the allosteric equilibrium between R and T states of the enzyme. In this article, the binding of substrates, substrate analogues, and nucleotides is studied, along with their effect on the R-T equilibrium by using highly deuterated, 1H,13C-methyl-labeled protein in concert with methyl-transverse relaxation optimized spectroscopy (TROSY) NMR. Although only the T state of the enzyme can be observed in spectra of wild-type unliganded aspartate transcarbamoylase, binding of active-site substrates shift the equilibrium so that correlations from the R state become visible, allowing the equilibrium constant (L') between ligand-saturated R and T forms of the enzyme to be measured quantitatively. The equilibrium constant between unliganded R and T forms (L) also is obtained, despite the fact that the R state is "invisible" in spectra, by means of an indirect process that makes use of relations that emerge from the fact that ligand binding and the R-T equilibrium are linked. Titrations with MgATP unequivocally establish that its binding directly perturbs the R-T equilibrium, consistent with the Monod-Wyman-Changeux model. This study emphasizes the utility of modern solution NMR spectroscopy in understanding protein function, even for systems with aggregate molecular masses in the hundreds of kilodaltons. 10.1073/pnas.0703347104

A suite of Mathematica notebooks for the analysis of protein main chain 15N NMR relaxation data

Spyracopoulos — 2007-01-19T05:41:44-00:00

Journal of Biomolecular NMR, Vol. 36, No. 4. (December 2006), pp. 215-224.

Model-free analysis for large proteins at high magnetic field strengths

Chang — 2007-09-14T16:29:15-00:00

Journal of Biomolecular NMR, Vol. 38, No. 4. (August 2007), pp. 315-324.

Real-time and equilibrium (19)F-NMR studies reveal the role of domain-domain interactions in the folding of the chaperone PapD.

JG Bann — 2008-04-14T17:59:35-00:00

Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 2. (22 January 2002), pp. 709-714.

PapD is a periplasmic chaperone essential for P pilus formation in pyelonephritic strains of E. coli. It is composed of two domains, each of which contains a tryptophan residue (Trp-36 and Trp-128, in the N- and C-terminal domains, respectively). To explore the role of domain-domain interactions during folding, the protein was labeled with 6-fluorotryptophan for use in (19)F-NMR experiments. (19)F-NMR data collected as a function of urea concentration revealed the presence of a resonance caused by Trp-128 that was distinct from either the folded or unfolded resonances. The time course of refolding from urea was monitored by stopped-flow fluorescence, CD, and (19)F-NMR, each method showing multiple kinetic phases. The (19)F-NMR stopped-flow spectra, collected at 70 microM of protein with a fluorine cryoprobe, demonstrated that the intermediate was populated early in the folding process (<5 s). The slow disappearance of the intermediate and unfolded resonance occurred at the same rate as the appearance of the native resonances of both domains. The data are consistent with a model in which the C-terminal domain collapses rapidly to an intermediate, whereas the stabilization of the final structure is slow and requires folding of the N-terminal domain with concomitant readjustment of the C-terminal domain structure.

Faithful estimation of dynamics parameters from CPMG relaxation dispersion measurements

Evgenii Kovrigin — 2008-06-02T01:37:56-00:00

Journal of Magnetic Resonance, Vol. 180, No. 1. (May 2006), pp. 93-104.

This work examines the robustness of fitting of parameters describing conformational exchange (kex, pa/b, and [Delta][omega]) processes from CPMG relaxation dispersion data. We have analyzed the equations describing conformational exchange processes for the intrinsic inter-dependence of their parameters that leads to the existence of multiple equivalent solutions, which equally satisfy the experimental data. We have used Monte-Carlo simulations and fitting to the synthetic data sets as well as the direct 3-D mapping of the parameter space of kex, pa/b, and [Delta][omega] to quantitatively assess the degree of the parameter inter-dependence. The demonstrated high correlation between parameters can preclude accurate dynamics parameter estimation from NMR spin-relaxation data obtained at a single static magnetic field. The strong parameter inter-dependence can readily be overcome through acquisition of spin-relaxation data at more than one static magnetic field thereby allowing accurate assessment of conformational exchange properties.

Cross-Correlated Relaxation Enhanced 1H-13C NMR Spectroscopy of Methyl Groups in Very High Molecular Weight Proteins and Protein Complexes

V Tugarinov — 2008-05-22T17:41:30-00:00

J. Am. Chem. Soc., Vol. 125, No. 34. (27 August 2003), pp. 10420-10428.

Abstract: A comparison of HSQC and HMQC pulse schemes for recording 1H-13C correlation maps of protonated methyl groups in highly deuterated proteins is presented. It is shown that HMQC correlation maps can be as much as a factor of 3 more sensitive than their HSQC counterparts and that the sensitivity gains result from a TROSY effect that involves cancellation of intra-methyl dipolar relaxation interactions. 1H-13C correlation spectra are recorded on U-[15N,2H], Ile1-[13C,1H] samples of (i) malate synthase G, a 723 residue protein, at 37 and 5 C, and of (ii) the protease ClpP, comprising 14 identical subunits, each with 193 residues (305 kDa), at 5 C. The high quality of HMQC spectra obtained in short measuring times strongly suggests that methyl groups will be useful probes of structure and dynamics in supramolecular complexes.

Dynamics of phosphate head groups in biomembranes. Comprehensive analysis using phosphorus-31 nuclear magnetic resonance lineshape and relaxation time measurements.

EJ Dufourc — 2008-05-20T22:37:25-00:00

Biophys. J., Vol. 61, No. 1. (1 January 1992), pp. 42-57.

Phospholipid head group dynamics have been studied by pulsed phosphorus-31 nuclear magnetic resonance (31P-NMR) of unoriented and macroscopically aligned dimyristoylphosphatidylcholine model membranes in the temperature range, 203-343 K. Lineshapes and echo intensities have been recorded as a function of interpulse delay times, temperature and macroscopic orientation of the bilayer normal with respect to the magnetic field. The dipolar proton-phosphorus (1H-31P) contribution to the transverse relaxation time, T2E, and to lineshapes was eliminated by means of a proton spin-lock sequence. In case of longitudinal spin relaxation, T1Z, the amount of dipolar coupling was evaluated by measuring the maximum nuclear Overhauser enhancement. Hence, the results could be analyzed by considering chemical shift anisotropy as the only relaxation mechanism. The presence of various minima both in T1Z and T2E temperature plots as well as the angular dependence of these relaxation times allowed description of the dynamics of the phosphate head group in the 31P-NMR time window, by three different motional classes, i.e., intramolecular, intermolecular and collective motions. The intramolecular motions consist of two hindered rotations and one free rotation around the bonds linking the phosphate head group to the glycerol backbone. These motions are the fastest in the hierarchy of time with correlation times varying from less than 10(-12) to 10(-6) s in the temperature range investigated. The intermolecular motions are assigned to phospholipid long axis rotation and fluctuation. They have correlation times ranging from 10(-11) s at high temperatures to 10(-3) s at low temperatures. The slowest motion affecting the 31P-NMR observables is assigned to viscoelastic modes, i.e., so called order director fluctuations and is only detected at high temperatures, above the main transition in pulse frequency dependent T2ECP experiments. Comprehensive analysis of the phosphate head group dynamics is achieved by a dynamic NMR model based on the stochastic Liouville equation. In addition to correlation times, this analysis provides activation energies and order parameters for the various motions, and a value for the bilayer elastic constant.

Estimates of methyl 13C and 1H CSA values (Deltasigma) in proteins from cross-correlated spin relaxation

Vitali Tugarinov — 2005-01-13T10:14:48-00:00

Journal of Biomolecular NMR, Vol. 30, No. 4., 397.

Motional properties of unfolded ubiquitin: a model for a random coil protein.

Julia Wirmer — 2006-10-05T00:23:36-00:00

J Biomol NMR (25 July 2006)

The characterization of unfolded states of proteins has recently attracted considerable interest, as the residual structure present in these states may play a crucial role in determining their folding and misfolding behavior. Here, we investigated the dynamics in the denatured state of ubiquitin in 8 M urea at pH2. Under these conditions, ubiquitin does not have any detectable local residual structure, and uniform (15)N relaxation rates along the sequence indicate the absence of motional restrictions caused by residual secondary structure and/or long-range interactions. A comparison of different models to predict relaxation data in unfolded proteins suggests that the subnanosecond dynamics in unfolded states depend on segmental motions only and do not show a dependence on the residue type but for proline and glycine residues.