Amide proton relaxation measurements employing a highly deuterated protein

Proton NMR longitudinal and transverse relaxation rates of unlabelled proteins are generally dominated by the many 1H-1H dipolar interactions so that spin diffusion, rather than molecular or internal motions, governs longitudinal relaxation. Here, relaxation measurements of backbone amide proton (1H(N)) magnetisations have been carried out employing the 99% 2H, 98% 15N labelled, small 2F2 protein domain in 10%/90% H(2)O/D(2)O solution. Under these conditions, the longitudinal relaxation rates exhibit time constants, T(1)*=1/R(1)* if described by a mono-exponential, within the range of 3.0 to 18.7s-a wide range which indicates that the phenomenon of spin diffusion has been greatly reduced. The majority of 1H(N) nuclei in this sample (pH 4.0 and 5 degrees C) exhibit chemical exchange with solvent that couples their longitudinal relaxation to that of the solvent. For the subset of 1H(N) nuclei not undergoing detectable solvent chemical exchange, the R(1)* rates correlate well with their individual 1H(N,O)/2H(N,O) structural environments. The correlation for corresponding transverse relaxation rates, R(2)* was found to be less good. Longitudinal relaxation measurements in 1%/99% H(2)O/D(2)O solution identify a further subset of 1H(N) nuclei which exhibit essentially indistinguishable R(1)* rates in both 1% and 10% H(2)O, implying that averaging of rates from spin diffusion processes and different 2F2 isotopomer populations are negligible for these 1H(N) sites. In addition to a high sensitivity to structural parameters, model calculations predict 1H(N) relaxation rates to exhibit pronounced sensitivity to internal dynamics.     

Brownian motion of nucleated cell envelopes impedes adhesion

We demonstrate that composite envelopes of nucleated cells exhibit pronounced short wavelength (相似文献   

Modeling diffusion of adsorbed polymer with explicit solvent

Computer simulations of a polymer chain of length N strongly adsorbed at the solid-liquid interface in the presence of explicit solvent are used to delineate the factors affecting the N dependence of the polymer lateral diffusion coefficient, D(||). We find that surface roughness has a large influence, and D(||) scales as D(||) approximately N(-x), with x approximately 3/4 and x approximately 1 for ideal smooth and corrugated surfaces, respectively. The first result is consistent with the hydrodynamics of a "particle" of radius of gyration R(G) approximately N(nu) (nu=0.75) translating parallel to a planar interface, while the second implies that the friction of the adsorbed chains dominates. These results are discussed in the context of recent measurements.     

Conformations of random polyampholytes

We study the size R(g) of random polyampholytes (i.e., polymers with randomly charged monomers) as a function of their length N. All results of our extensive Monte Carlo simulations can be rationalized in terms of the scaling theory we develop for the Kantor-Kardar necklace model, although this theory neglects the quenched disorder in the charge sequence along the chain. We find approximately N1/2. The elongated globule model, the initial predictions of both Higgs and Joanny ( approximately N1/3) and Kantor and Kardar ( approximately N), and previous numerical estimates are ruled out.     

Spectral energy dynamics in magnetohydrodynamic turbulence

Spectral direct numerical simulations of incompressible MHD turbulence at a resolution of up to 1024(3) collocation points are presented for a statistically isotropic system as well as for a setup with an imposed strong mean magnetic field. The spectra of residual energy, E(R)k=|E(M)k - E(K)k|, and total energy, Ek=E(K)k+E(M)k, are observed to scale self-similarly in the inertial range as E(R)k approximately k(-7/3), E(k)approximately k(-5/3) (isotropic case) and E(R)(k(perpendicular) approximately k(-2)(perpendicular), E(k(perpendicular))approximately k(-3/2)(perpendicular) (anisotropic case, perpendicular to the mean field direction). A model of dynamic equilibrium between kinetic and magnetic energy, based on the corresponding evolution equations of the eddy-damped quasinormal Markovian closure approximation, explains the findings. The assumed interplay of turbulent dynamo and Alfvén effect yields E(R)k approximately kE2(k), which is confirmed by the simulations.     

A pulse EPR study of longitudinal relaxation of the stable radical in gamma-irradiated L-alanine

The longitudinal relaxation rate of the first stable alanine radical, SAR1, was studied by employing pulse EPR technique over a wide temperature interval (5-290 K). The complex nonexponential recovery of the longitudinal magnetization in this temperature interval has been described with two characteristic relaxation times, 1/T*(1a) as the faster component and 1/T*(1b) as the slower component, respectively. It was shown that 1/T*(1a) is strongly affected by the CH(3) group dynamics of the SAR1 center. The complete temperature dependence of 1/T*(1a) was described by invoking several relaxation mechanisms that involve hindered motion of the CH(3) group from classical rotational motion to coherent rotational tunneling. It was shown that all relevant relaxation mechanisms are determined by a single correlation time with the potential barrier (Delta E/k=1570 K). On the other hand the temperature dependence of 1/T*(1b) is related to the motional dynamics of the neighborly NH(3) and CH(3) groups. We found a larger average potential barrier for this motion (Delta E/k=2150 K) corresponding to smaller tunneling frequencies of the neighbor groups.     

Slow spin relaxation of Rb atoms confined in glass cells filled with dense 4He gas at 1.85 K

At temperatures below 2.1 K, long-lived gaseous Rb atoms in glass cells have been generated with a simple method: irradiating the cells, containing 4He gas and Rb metal, with a cw laser. The obtained atomic Rb density ( approximately 10(8) cm(-3)) decreases with a 1/e time constant of about 10 s at 1.85 K. We have performed optical pumping of the Rb atoms and measured the longitudinal electronic spin relaxation time at 1.85 K as well. For processes (such as Rb-He collisions) which do not remove the atomic Rb from the vapor, this relaxation time is found to be about 60+/-15 s.     

The matrix formalism for generalised gradients with time-varying orientation in diffusion NMR

Protein backbone 15N NMR spin relaxation rates are useful in characterizing the protein dynamics and structures. To observe the protein nuclear-spin resonances a pulse sequence has to include a water suppression scheme. There are two commonly employed methods, saturating or dephasing the water spins with pulse field gradients and keeping them unperturbed with flip-back pulses. Here different water suppression methods were incorporated into pulse sequences to measure 15N longitudinal T1 and transversal rotating-frame T1ρ spin relaxation. Unexpectedly the 15N T1 relaxation time constants varied significantly with the choice of water suppression method. For a 25-kDa Escherichiacoli. glutamine binding protein (GlnBP) the T1 values acquired with the pulse sequence containing a water dephasing gradient are on average 20% longer than the ones obtained using a pulse sequence containing the water flip-back pulse. In contrast the two T1ρ data sets are correlated without an apparent offset. The average T1 difference was reduced to 12% when the experimental recycle delay was doubled, while the average T1 values from the flip-back measurements were nearly unchanged. Analysis of spectral signal to noise ratios (s/n) showed the apparent slower 15N relaxation obtained with the water dephasing experiment originated from the differences in 1HN recovery for each relaxation time point. This in turn offset signal reduction from 15N relaxation decay. The artifact becomes noticeable when the measured 15N relaxation time constant is comparable to recycle delay, e.g., the 15N T1 of medium to large proteins. The 15N relaxation rates measured with either water suppression schemes yield reasonable fits to the structure. However, data from the saturated scheme results in significantly lower Model-Free order parameters (=0.81) than the non-saturated ones (=0.88), indicating such order parameters may be previously underestimated.     

Universality of Uhrig dynamical decoupling for suppressing qubit pure dephasing and relaxation

The optimal N-pulse dynamical decoupling discovered by Uhrig for a spin-boson model [Phys. Rev. Lett. 98, 100504 (2007)10.1103/PhysRevLett.98.100504] is proved to be universal in suppressing to O(T;{N+1}) the pure dephasing or the longitudinal relaxation of a qubit (or spin 1/2) coupled to a generic bath in a short-time evolution of duration T. For suppressing the longitudinal relaxation, a Uhrig pi-pulse sequence can be generalized to be a superposition of the ideal Uhrig pi-pulse sequence as the core and an arbitrarily shaped pulse sequence satisfying certain symmetry requirements. The generalized Uhrig dynamical decoupling offers the possibility of manipulating the qubit while simultaneously combating the longitudinal relaxation.     

Proton relaxation enhancement by means of serum albumin and poly-L-lysine labeled with DTPA-Gd3+: relaxivities as a function of molecular weight and conjugation efficiency.

A series of poly-L-lysine chains, with molecular weight ranging from 3300 up to 102,000 Da, were labeled with DTPA-Gd3+. No significant differences in longitudinal and transversal relaxivity, could be demonstrated as a function of the chain length. The R1 and R2 relaxivities were respectively 2.5 and 5 times superior to those of plain DTPA-Gd3+ (at 2.4 T). Bovine serum albumin was also labeled in a way that a wide (DTPA-Gd3+)/BSA range (3-39) was obtained. The longitudinal relaxivity, of these paramagnetically labeled albumins, increased with increasing (DTPA-Gd3+)/BSA ratios. This effect was most pronounced at very low (DTPA-Gd3+)/BSA ratios.     

Characteristics of driven polymer surfaces: growth and roughness

Using a Monte Carlo simulation, the growth and roughness characteristics of polymer surfaces are studied in 2+1 dimensions. Kink-jump and reptation dynamics are used to move polymer chains under a driving field where they deposit onto an impenetrable attractive wall. Effects of field (E), chain length (L(c)), and the substrate size (L) on the growing surfaces are studied. In low field, the interface width (W) shows a crossover from one power-law growth in time (W approximately t(beta(1))) to another (W approximately t(beta(2))), before reaching its asymptotic value (W(s)), with beta(1)( approximately 0.5+/-0.1)相似文献   

An iterative fitting procedure for the determination of longitudinal NMR cross-correlation rates

We present a method to measure (15)N-(1)H dipolar/(15)N CSA longitudinal cross-correlation rates in protonated proteins. The method depends on the measurement of four observables: the cumulative proton-proton cross relaxation rates, the (15)N R(1) relaxation rate, the multiexponential decay of 2N(Z)H(N)(Z) spin-order, and multiexponential buildup of 2N(Z)H(N)(Z) spin-order. The (15)N-(1)H dipolar/(15)N CSA longitudinal cross-correlation rate is extracted from these measurements by an iterative fitting procedure to the solution of differential equations describing the coupled relaxation dynamics of the z-magnetization of the (15)N nucleus, the two-spin-order 2N(Z)H(N)(Z), and a two-spin-order term 2N(Z)H(Q)(Z) describing the interaction with remote protons. The method is applied to the microbial ribonuclease binase. The method can also extract longitudinal cross-correlation rates for those amide protons that are involved in rapid solvent exchange. The experiment that serves for extracting proton-proton cross-relaxation rates is a modification of 3D (15)N-resolved NOESY-HSQC. The experiment restores the solvent magnetization to its equilibrium state during data detection for all phase cycling steps and all values of NOE mixing times and is recommended for use in standard applications as well.     

Echo-spacing optimization for the simultaneous measurement of reversible (R2') and irreversible (R2) transverse relaxation rates

Accurate measurement of reversible (R2') and irreversible (R2) transverse relaxation rates plays a key role in various magnetic resonance imaging research and applications. Although optimization of echo spacing for a multiecho pulse sequence measuring a single exponential decay has been investigated, optimization in sequences such as Gradient-Echo Sampling of Free Induction Decay and Echo (GESFIDE), in which two echo trains are simultaneously measured to obtain both R2 and R2', has not been reported. In this work, optimum echo spacings for the GESFIDE sequence are determined to improve the accuracy of measured relaxation parameters. Various relaxation rates and the number of acquired echoes are considered, as well as whether the receiver bandwidth is kept fixed or is varied with echo spacing. In the case of constant receiver bandwidth, results show that the echo train length approximately equal to T2* should be used for each echo train in GESFIDE to minimize uncertainty in R2 or R2'. If the receiver bandwidth is allowed to change with echo spacing in order to maximize the image signal-to-noise ratio, the optimum echo train length will vary, generally increasing with the number of echoes.     

Evaluation of CH3-DTPA-Gd (NMS60) as a new MR contrast agent: early phase II study in brain tumors and dual dynamic contrast-enhanced imaging

PURPOSE: A newly developed contrast material, CH3-DTPA-Gd (NMS60), a trimer containing 3 Gd(3+) atoms per molecule, has been shown to offer greater enhancement and longer vascular retention than gadopentetate dimeglumine (Gd-DTPA) in animals. We report on our early phase II study on NMS60 in brain tumor patients together with supplementary investigations. METHODS AND MATERIALS: The longitudinal relaxation rate (R(1)=1/T(1)) and the transverse relaxation rate (R(2)*=1/T(2)*) of NMS60 and Gd-DTPA were determined at 20 degrees C in water at 1.5 T. An NMS60 dose of 0.1 or 0.2 mmol (Gd)/kg was randomly assigned and administered to 10 patients (five women, five men; mean age: 49 years) with brain tumors. Safety and contrast-enhancing ability of NMS60 were evaluated. Dual dynamic contrast-enhanced T(1) and R(2)* studies (DUCE imaging) were also carried out in two patients. RESULTS: Regarding the relaxivity per Gd, R(1) and R(2)* of NMS60 were 9.5 and 11.0 (mmol/L x s)(-1), respectively, compared to 4.8 and 7.2 (mmol/L x s)(-1) for Gd-DTPA. Although a transient slight increase of alanine aminotransferase was observed in one case, no other adverse reactions were observed after administration of NMS60. Contrast enhancement by NMS60 was excellent at both concentrations, and when tumor detectability was assessed with a five-point scale, the diagnostic usefulness was 4 or higher in all cases. In DUCE imaging, NMS60 appeared to show high signal intensity, when compared with the data obtained separately for Gd-DTPA. CONCLUSION: NMS60 had a high contrasting effect and little toxicity, and is expected to be clinically useful.     

Accurate statistics of a flexible polymer chain in shear flow

We present exact and analytically accurate results for the problem of a flexible polymer chain in shear flow. Under such a flow the polymer tumbles, and the probability distribution of the tumbling times tau of the polymer decays exponentially as approximately exp(-alphatau/tau_{0}) (where tau_{0} is the longest relaxation time). We show that for a Rouse chain this nontrivial constant alpha can be calculated in the limit of a large Weissenberg number (high shear rate) and is in excellent agreement with our simulation result of alpha approximately 0.324. We also derive exactly the distribution functions for the length and the orientational angles of the end-to-end vector R of the polymer.     

Dynamics of chain molecules in disordered materials

The dynamic behavior of hard chains in disordered materials composed of fixed hard spheres is studied using discontinuous molecular dynamics simulations. The matrix induces entanglements in the chain fluid, i.e., for high matrix densities the diffusion coefficient D scales with the chain length N as D is approximately N(-2). At high matrix densities the rotational relaxation time becomes very large but the translational diffusion is not affected significantly; i.e., the chains display a dynamic heterogeneity reminiscent of probe diffusion in supercooled liquids and glasses. We show that this is because some chains are trapped, and move via a hopping mechanism. There are no signatures of this dynamic heterogeneity in the matrix static structure, however, which is identical to that of a hard-sphere liquid.     

Investigation of longitudinal 31P relaxation in metal selenophosphate compounds

Molten salt syntheses yield a rich variety of metal selenophosphate compounds which have a wide range of 31P T(1) longitudinal relaxation times (20-3000 s). There is a qualitative positive correlation between squared dipolar couplings and 1/T(1), suggesting that these interactions contribute to relaxation. However, two of the compounds, K(2)CdP(2)Se(6) and Rb(2)CdP(2)Se(6), have T(1) which are significantly shorter than what is expected from dipolar couplings. The ESR spectra of these compounds show the presence of unpaired electrons which may accelerate the rate of 31P relaxation. The importance of relaxation in application of (31)P NMR to these systems is demonstrated in analysis of the mixture of crystalline products formed in a Ag(4)P(2)Se(6) synthesis. At short relaxation delays, the NMR intensities are non-quantitative and overestimate the concentration of an Ag(7)PSe(6) impurity.     

Analysis of 1H-NMR relaxation time distributions in L1 to L6 rat lumbar vertebrae

A better knowledge of the NMR relaxation behavior of bone tissue can improve the definition of imaging protocols to detect bone diseases like osteoporosis. The six rat lumbar vertebrae, from L1 to L6, were analyzed by means of both transverse (T(2)) and longitudinal (T(1)) relaxation of (1)H nuclei at 20 MHz and 30 degrees C. Distributions of relaxation times, computed using the multiexponential inversion software uniform penalty inversion, extend over decades for both T(2) and T(1) relaxation. In all samples, the free induction decay (FID) from an inversion-recovery (IR) T(1) measurement shows an approximately Gaussian (solid-like) component, exp[-1/2(t/T(GC))2], with T(GC) approximately 12 micros (GC for Gaussian component) and a liquid-like component (LLC) with initially simple-exponential decay. Averaging and smoothing procedures are adopted to obtain the ratio alpha between GC and LLC signals and to get separate T(1) distributions for GC and LLC. Distributions of T(1) for LLC show peaks centered at 300-500 ms and shoulders going down to 10 ms, whereas distributions of T(1) for GC are single broad peaks centered at roughly 100 ms. The T(2) distributions by Carr-Purcell-Meiboom-Gill at 600 micros echo spacing are very broad and extend from 1 ms to hundreds of ms. This long echo spacing does not allow one to see a peak in the region of hundreds of micros, which is better seen by single spin-echo T(2) measurements. Results of the relaxation analysis were then compared with densitometric data. From the study, a clear picture of the intratrabecular and intertrabecular (1)H signals emerges. In particular, the GC is presumed to be due to (1)H in collagen, LLC due to all the fluids in the bone including water and fat, and the very short T(2) peak due to the intratrabecular water. Overall, indications of some trends in composition and in pore-space distributions going from L1 to L6 appeared. Published results on rat vertebrae obtained by fitting the curves by discrete two-component models for both T(2) and T(1) are consistent with our results and can be better interpreted in light of the shown distributions of relaxation times.     

Transverse relaxation in the rotating frame induced by chemical exchange

In the presence of radiofrequency irradiation, relaxation of magnetization aligned with the effective magnetic field is characterized by the time constant T1rho. On the other hand, the time constant T2rho characterizes the relaxation of magnetization that is perpendicular to the effective field. Here, it is shown that T2rho can be measured directly with Carr-Purcell sequences composed of a train of adiabatic full-passage (AFP) pulses. During adiabatic rotation, T2rho characterizes the relaxation of the magnetization, which under adiabatic conditions remains approximately perpendicular to the time-dependent effective field. Theory is derived to describe the influence of chemical exchange on T2rho relaxation in the fast-exchange regime, with time constant defined as T2rho,ex. The derived theory predicts the rate constant R2rho,ex (= 1/T2rho,ex) to be dependent on the choice of amplitude- and frequency-modulation functions used in the AFP pulses. Measurements of R2rho,ex of the water/ethanol exchanging system confirm the predicted dependence on modulation functions. The described theoretical framework and adiabatic methods represent new tools to probe exchanging systems.