Cooling overall spin temperature: protein NMR experiments optimized for longitudinal relaxation effects

In experiments performed on protonated proteins at high fields, 80% of the NMR spectrometer time is spent waiting for the ¹H atoms to recover their polarization after recording the free induction decay. Selective excitation of a fraction of the protons in a large molecule has previously been shown to lead to faster longitudinal relaxation for the selected protons [K. Pervushin, B. Vögeli, A. Eletsky, Longitudinal ¹H relaxation optimization in TROSY NMR spectroscopy, J. Am. Chem. Soc. 124 (2002) 12898–12902; P. Schanda, B. Brutscher, Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014–8015; H.S. Attreya, T. Szyperski, G-matrix Fourier transform NMR spectroscopy for complete protein resonance assignment, Proc. Natl. Acad. Sci. USA 101 (2004) 9642–9647]. The pool of non-selected protons acts as a “thermal bath” and spin-diffusion processes (“flip-flop” transitions) channel the excess energy from the excited pool to the non-selected protons in regions of the molecule where other relaxation processes can dissipate the excess energy. We present here a sensitivity enhanced HSQC sequence (COST-HSQC), based on one selective E-BURP pulse, which can be used on protonated ¹⁵N enriched proteins (with or without ¹³C isotopic enrichment). This experiment is compared to a gradient sensitivity enhanced HSQC with a water flip-back pulse (the water flip-back pulse quenches the spin diffusion between ¹H^N and ¹H^α spins). This experiment is shown to have significant advantages in some circumstances. Some observed limitations, namely sample overheating with short recovery delays and complex longitudinal relaxation behaviour are discussed and analysed.     

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.     

Flip-back, an old trick to face highly contrasted relaxation times: application in the characterization of pharmaceutical mixtures by CPMAS NMR

The ¹³C–¹H CPMAS with flip-back pulse NMR experiment is revisited in view of applications to pharmaceutical mixtures. The analysis of the kinetics of relaxation and CP transfer with and without the flip-back pulse shows that a significant gain in ¹³C signal can be expected (thus in experimental time) from the flip-back pulse for protons with long T₁. The gain is of the order of T₁ of the protons expressed in seconds. The experiment is applied on samples with highly contrasted spin-lattice relaxation times T₁ for protons, situation encountered in pharmaceutical mixtures. The application of the flip-back increases significantly the relative signal intensity of the component with the longer T₁, making this component detectable even after using short recycle delays. Therefore, this CPMAS with flip-back experiment could be used routinely to get ¹³C CPMAS NMR spectra of mixtures in constant experimental time and signal-to-noise ratio without the need for optimization of the recycle delays, and for whatever may be the degree of crystallinity of the active principal ingredient (API) and/or excipients.     

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

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 (15)N 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.     

Water diffusion-exchange effect on the paramagnetic relaxation enhancement in off-resonance rotating frame

The off-resonance rotating frame technique based on the spin relaxation properties of off-resonance T1rho can significantly increase the sensitivity of detecting paramagnetic labeling at high magnetic fields by MRI. However, the in vivo detectable dimension for labeled cell clusters/tissues in T1rho-weighted images is limited by the water diffusion-exchange between mesoscopic scale compartments. An experimental investigation of the effect of water diffusion-exchange between compartments on the paramagnetic relaxation enhancement of paramagnetic agent compartment is presented for in vitro/in vivo models. In these models, the size of paramagnetic agent compartment is comparable to the mean diffusion displacement of water molecules during the long RF pulses that are used to generate the off-resonance rotating frame. The three main objectives of this study were: (1) to qualitatively correlate the effect of water diffusion-exchange with the RF parameters of the long pulse and the rates of water diffusion, (2) to explore the effect of water diffusion-exchange on the paramagnetic relaxation enhancement in vitro, and (3) to demonstrate the paramagnetic relaxation enhancement in vivo. The in vitro models include the water permeable dialysis tubes or water permeable hollow fibers embedded in cross-linked proteins gels. The MWCO of the dialysis tubes was chosen from 0.1 to 15 kDa to control the water diffusion rate. Thin hollow fibers were chosen to provide sub-millimeter scale compartments for the paramagnetic agents. The in vivo model utilized the rat cerebral vasculatures as a paramagnetic agent compartment, and intravascular agents (Gd-DTPA)30-BSA were administrated into the compartment via bolus injections. Both in vitro and in vivo results demonstrate that the paramagnetic relaxation enhancement is predominant in the T1rho-weighted image in the presence of water diffusion-exchange. The T1rho contrast has substantially higher sensitivity than the conventional T1 contrast in detecting paramagnetic agents, especially at low paramagnetic agent volumetric fractions, low paramagnetic agent concentrations, and low RF amplitudes. Short pulse duration, short pulse recycle delay and efficient paramagnetic relaxation can reduce the influence of water diffusion-exchange on the paramagnetic enhancement. This study paves the way for the design of off-resonance rotating experiments to detect labeled cell clusters/tissue compartments in vivo at a sub-millimeter scale.     

固体核磁共振中膜蛋白双交叉极化效率与动力学参数相关的定量分析

固体核磁共振（NMR）中双交叉极化（DCP）是用于膜蛋白信号指认的多维异核相关实验的基本技术模块.DCP的效率在很大程度上决定了多维异核相关实验的效率.本文分析了3种典型的膜环境中的膜蛋白（AQPZ、DAGK和EV71 2B）的DCP效率及其影响因素.结果显示,在相同的实验条件下,3种蛋白样品的DCP效率存在明显差异：其中AQPZ的DCP效率最高（31%）,DAGK的效率次之（23%）,EV71 2B的效率最低（14%）.通过测量它们在旋转坐标下的自旋-晶格弛豫时间（T_1ρ）和偶极耦合常数（D_HN）,发现膜蛋白的运动会明显缩短T_1ρ,但对D_HN的影响较小.在实验的基础上,建立了T_1ρ与DCP效率相关的模型,并基于DCP动力学的定量分析,证明了运动导致的T_1ρ缩短是降低DCP效率的主要原因.因此,可以通过定量分析未知样品的T_1ρ来预测其DCP的最优效率,为DCP实验的优化提供依据.     

NMR spin locking of proton magnetization under a frequency-switched Lee-Goldburg pulse sequence

The spin dynamics of NMR spin locking of proton magnetization under a frequency-switched Lee-Goldburg (FSLG) pulse sequence is investigated for a better understanding of the line-narrowing mechanism in PISEMA experiments. For the sample of oriented 15N(1,3,5,7)-labeled gramicidin A in hydrated DMPC bilayers, it is found that the spin-lattice relaxation time T(1rho)(H) in the tilted rotating frame is about five times shorter when the 1H magnetization is spin locked at the magic angle by the FSLG sequence compared to the simple Lee-Goldburg sequence. It is believed that the rapid phase alternation of the effective fields during the FSLG cycles results in averaging of the spin lock field so that the spin lock becomes less efficient. A FSLG supercycle has been suggested here to slow the phase alternation. It has been demonstrated experimentally that a modified PISEMA pulse sequence with such supercycles gives rise to about 30% line narrowing in the dipolar dimension in the PISEMA spectra compared to a standard PISEMA pulse sequence.     

Investigation of the effect of a variety of pulse errors on spin I=1 quadrupolar alignment echo spectroscopy

We report on an analysis of a well known three-pulse sequence for generating and detecting spin I=1 quadrupolar order when various pulse errors are taken into account. In the situation of a single quadrupolar frequency, such as the case found in a single crystal, we studied the potential leakage of single and/or double quantum coherence when a pulse flip error, finite pulse width effect, RF transient or a resonance offset is present. Our analysis demonstrates that the four-step phase cycling scheme studied is robust in suppressing unwanted double and single quantum coherence as well as Zeeman order that arise from the experimental artifacts, allowing for an unbiased measurement of the quadrupolar alignment relaxation time, T(1Q). This work also reports on distortions in quadrupolar alignment echo spectra in the presence of experimental artifacts in the situation of a powdered sample, by simulation. Using our simulation tool, it is demonstrated that the spectral distortions associated with the pulse artifacts may be minimized, to some extent, by optimally choosing the time between the first two pulses. We highlight experimental results acquired on perdeuterated hexamethylbenzene and polyethylene that demonstrate the efficacy of the phase cycling scheme for suppressing unwanted quantum coherence when measuring T(1Q). It is suggested that one employ two separate pulse sequences when measuring T(1Q) to properly analyze the short time behavior of quadrupolar alignment relaxation data.     

Improvement of duty-cycle heating compensation in NMR spin relaxation experiments

To reliably measure NMR relaxation properties of macromolecules is a prerequisite for precise experiments that identify subtle variations in relaxation rates, as required for the determination of rotational diffusion anisotropy, CSA tensor determination, advanced motional modeling or entropy difference estimations. An underlying problem with current NMR relaxation measurement protocols is maintaining constant sample temperature throughout the execution of the relaxation series especially when rapid data acquisition is required. Here, it is proposed to use a combination of a heating compensation and a proton saturation sequence at the beginning of the NMR relaxation pulse scheme. This simple extension allows reproducible, robust and rapid acquisition of NMR spin relaxation data sets. The method is verified with (15)N spin relaxation measurements for human ubiquitin.     

Relaxation-induced dipolar exchange with recoupling-An MAS NMR method for determining heteronuclear distances without irradiating the second spin

A new magic-angle spinning NMR method for distance determination between unlike spins, where one of the two spins in question is not irradiated at all, is introduced. Relaxation-induced dipolar exchange with recoupling (RIDER) experiments can be performed with conventional double-resonance equipment and utilize the familiar π-pulse trains to recouple the heteronuclear dipolar interaction under magic-angle spinning conditions. Longitudinal relaxation of the passive spin during a delay between two recoupling periods results in a dephasing of the heteronuclear coherence and consequently a dephasing of the magnetization detected after the second recoupling period. The information about the dipolar coupling is obtained by recording normalized dephasing curves in a fashion similar to the REDOR experiment. At intermediate mixing times, the dephasing curves also depend on the relaxation properties of the passive spin, i.e., on single- and double-quantum longitudinal relaxation times for the case of I = 1 nuclei, and these relaxation times can be estimated with this new method. To a good approximation, the experiment does not depend on possible quadrupolar interactions of the passive spin, which makes RIDER an attractive method when distances to quadrupolar nuclei are to be determined. The new method is demonstrated experimentally with ¹⁴N and ²H as heteronuclei and observation of ¹³C in natural abundance.     

Dependencies of multi-component T2 and T1ρ relaxation on the anisotropy of collagen fibrils in bovine nasal cartilage

Both NMR spectroscopy and MRI were used to investigate the dependencies of multi-component T2 and T1ρ relaxation on the anisotropy of bovine nasal cartilage (BNC). The non-negative least square (NNLS) method and the multi-exponential fitting method were used to analyze all experimental data. When the collagen fibrils in nasal cartilage were oriented at the magic angle (55°) to the magnetic field B0, both T2 and T1ρ were single component, regardless of the spin-lock field strength or the echo spacing time in the pulse sequences. When the collagen fibrils in nasal cartilage were oriented at 0° to B0, both T2 and T1ρ at a spin-lock field of 500 Hz had two components. When the spin-lock field was increased to 1000 Hz or higher, T1ρ relaxation in nasal cartilage became a single component, even when the specimen orientation was 0°. These results demonstrate that the specimen orientation must be considered for any multi-component analysis, even for nasal cartilage that is commonly considered homogenously structured. Since the rapidly and slowly relaxing components can be attributed to different portions of the water population in tissue, the ability to resolve different relaxation components could be used to quantitatively examine individual molecular components in connective tissues.     

Effective dipolar couplings determined by dipolar dephasing of double-quantum coherences

It is shown how homonuclear distances and homonuclear dipolar lattice sums between spin-1/2 nuclei can be measured by a pulsed solid-state NMR experiment under magic-angle spinning conditions. The presented technique is based on double-quantum coherence filtering. Instead of measuring a build-up of double-quantum coherence the pulse sequence is designed to dephase double-quantum coherence. This is achieved by exciting double-quantum coherence either with the help of the through-space dipolar coupling or the through-bond dipolar coupling while the dephasing relies on the through-space dipolar coupling as selected by a gamma-encoded pulse sequence from the C/R symmetry class. Since dephasing curves can be normalized on zero dephasing, it is possible to analyze the initial dephasing regime and hence determine dipolar lattice sums (effective dipolar couplings) in multiple-spin systems. A formula for the effective dipolar coupling is derived theoretically and validated by numerical calculations and experiments on crystalline model compounds for (13)C and (31)P spin systems. The double-quantum dephasing experiment can be combined with constant-time data sampling to compensate for relaxation effects, consequently only two experimental data points are necessary for a single distance measurement. The phase cycling overhead for the constant-time experiment is minimal because a short cogwheel phase cycle exists. A 2D implementation is demonstrated on [(13)C(3)]alanine.     

Three-dimensional protein NMR TROSY-type (15)N-resolved (1)H(N)-(1)H(N) NOESY spectra with diagonal peak suppression

An earlier two-dimensional NOESY experiment with diagonal peak suppression in the (1)H(N)-(1)H(N) region is extended to three dimensions by including (15)N evolution while maintaining the TROSY approach throughout. The technique suppresses all anti-TROSY resonances by appropriate pulse sequence elements and for large molecules at high fields possible semi- and anti-TROSY artifacts are further suppressed by virtue of much shorter transverse relaxation times for these components. The new technique is demonstrated using an (15)N-labeled protein sample, RAP 17-97 (N-terminal domain of alpha2-macroglobulin Receptor Associated Protein), in H(2)O at 500 MHz.     

The equivalence between off-resonance and on-resonance pulse sequences and its application to steady-state free precession with diffusion in inhomogeneous fields

We show that the spin dynamics of any pulse sequence with off-resonant pulses is identical to that of a modified sequence with on-resonant pulses, including relaxation and diffusion effects. This equivalence applies to pulse sequences with arbitrary offset frequency deltaomega(0) which may exceed the RF field strength omega(1). Using this approach, we examine steady-state free precession (SSFP) in grossly inhomogeneous fields. We show explicitly that the magnitude of the magnetization for each mode at an offset frequency deltaomega(0) is equal to that for SSFP with on-resonance pulses of rescaled amplitude, with the same dependence on relaxation times and diffusion coefficient. The rescaling depends on offset frequency and RF field strength. The theoretical results have been tested experimentally and excellent agreement is found.     

Selection of pulse sequences producing maximum tissue contrast in magnetic resonance imaging

The importance of spin density [N(H)] and spin-lattice (T₁) and spin-spin (T₂) relaxation in the characterization of tissue by nuclear magnetic resonance (NMR) is clearly recognized. This work considers which optimized pulse sequences provide the best tissue discrimination between a given pair of tissues. The effects of tissue spin density and machine-imposed minimum rephasing echo times (TE_MIN) for achieving maximum signal tissue contrast are discussed. A long TE_MIN sacrifices T₁-dependent contrast in saturation recovery (SR) and inversion recovery (IR) pulse sequences so that spin-echo (SE) becomes the optimum sequence to provide tissue contrast, due to T₂ relaxation. Pulse sequences providing superior performance may be selected based on spin density and T₁ and T₂ ratios for a given pair of tissues. Selection of the preferred pulse sequence and interpulse delay times to produce maximum tissue contrast is strongly dependent on knowledge of tissue spin densities as well as T₁ and T₂ characteristics. As the spin density ratio increases, IR replaces SR as the preferred sequence and SE replaces IR and SR as the pulse sequence providing superior contrast. To select the optimal pulse sequence and interpulse delay times, an accurate knowledge of tissue spin density, T₁ and T₂ must be known for each tissue.     

Sensitivity enhancement using paramagnetic relaxation in MAS solid-state NMR of perdeuterated proteins

Previously, Ishii et al., could show that chelated paramagnetic ions can be employed to significantly decrease the recycle delay of a MAS solid-state NMR experiment [N.P. Wickramasinghe, M. Kotecha, A. Samoson, J. Past, Y. Ishii, Sensitivity enhancement in C-13 solid-state NMR of protein microcrystals by use of paramagnetic metal ions for optimizing H-1 T-1 relaxation, J. Magn. Reson. 184 (2007) 350-356]. Application of the method is limited to very robust samples, for which sample stability is not compromised by RF induced heating. In addition, probe integrity might be perturbed in standard MAS PRE experiments due to the use of very short duty cycles. We show that these deleterious effects can be avoided if perdeuterated proteins are employed that have been re-crystallized from D(2)O:H(2)O=9:1 containing buffer solutions. The experiments are demonstrated using the SH3 domain of chicken alpha-spectrin as a model system. The labeling scheme allows to record proton detected (1)H, (15)N correlation spectra with very high resolution in the absence of heteronuclear dipolar decoupling. Cu-edta as a doping reagent yields a reduction of the recycle delay by up to a factor of 15. In particular, we find that the (1)H T(1) for the bulk H(N) magnetization is reduced from 4.4s to 0.3s if the Cu-edta concentration is increased from 0mM to 250 mM. Possible perturbations like chemical shift changes or line broadening due to the paramagnetic chelate complex are minimal. No degradation of our samples was observed in the course of the experiments.     

Decay of dipolar order in diamagnetic and paramagnetic proteins and protein gels

Magnetic relaxation in solids may be complicated by the creation and loss of dipolar order at finite rates. In tissues the molecular and spin dynamics may be significantly different because of the relatively high concentration of water. We have applied a modified Jeneer-Broekaert pulse sequence to measure dipolar relaxation rates in both dry and hydrated protein systems that may serve as magnetic models for tissue. In lyophilized and dry serum albumin, the dipolar relaxation time, T(1D) is on the order of 1 ms and is consistent with earlier reports. When hydrated by deuterium oxide, the dipolar relaxation times measured were on the order of tens of microseconds. When paramagnetic centers are included in the protein, the Jeneer-Broekaert echo decay times became the order of the decay time for transverse magnetization, i.e., the order of 10 micros or less. In the hydrated or paramagnetic systems, the dipolar relaxation times are too short to require inclusion in the quantitative analysis of magnetization transfer experiments.     

2CALIS doubling the sensitivity of CALIS for calibration of the rf field strength for indirectly observed nuclei

A new set of pulse sequences, 2CALIS, that exhibit double sensitivity of the recent CALIS pulse sequences for accurate calibration of the rf field strength for an indirectly observed spin is introduced. The sensitivity gain is a result of not forming heteronuclear coherence transfer gradient echoes although they are excellent for artifact suppression. It is, however, demonstrated that the scheme in 2CALIS for suppression of non (13)C-attached proton magnetization is adequate for calibration of the (13)C rf field strength even on natural abundance samples. A 2CALIS version with Watergate applicable to biomolecules in aqueous solution is also presented and demonstrated both in (13)C natural abundance and on a (13)C, (15)N enriched protein sample.     

An investigation of the origins of contrast in NMR spin echo images of plant tissue.

The effects that the spatial distribution of water protons and their transverse relaxation times have on the image contrast of spin echo images of courgette was investigated. The T2-weighted image of courgette contains the most anatomical information. The image contrast was explained using a phenomenological theory based on the Bloch equations, which gave an insight into the morphology and microdynamics of water in the plant tissue. The perceived contrast in the spin echo images of courgette, glucose and Sephadex bead solutions can be dramatically altered by keeping all the imaging acquisition parameters constant, such as the recycle and echo time, but reducing the interpulse spacing by introducing a CPMG train of 180 degrees pulses into the middle of the sequence. These changes were interpreted by considering the microenvironment of the water. This work demonstrates that the origin of image contrast in T2-weighted images of plant tissue can be understood using the water proton transverse relaxation theory developed by Hills et al.