Correction of spin diffusion during iterative automated NOE assignment

Indirect magnetization transfer increases the observed nuclear Overhauser enhancement (NOE) between two protons in many cases, leading to an underestimation of target distances. Wider distance bounds are necessary to account for this error. However, this leads to a loss of information and may reduce the quality of the structures generated from the inter-proton distances. Although several methods for spin diffusion correction have been published, they are often not employed to derive distance restraints. This prompted us to write a user-friendly and CPU-efficient method to correct for spin diffusion that is fully integrated in our program ambiguous restraints for iterative assignment (ARIA). ARIA thus allows automated iterative NOE assignment and structure calculation with spin diffusion corrected distances. The method relies on numerical integration of the coupled differential equations which govern relaxation by matrix squaring and sparse matrix techniques. We derive a correction factor for the distance restraints from calculated NOE volumes and inter-proton distances. To evaluate the impact of our spin diffusion correction, we tested the new calibration process extensively with data from the Pleckstrin homology (PH) domain of Mus musculus beta-spectrin. By comparing structures refined with and without spin diffusion correction, we show that spin diffusion corrected distance restraints give rise to structures of higher quality (notably fewer NOE violations and a more regular Ramachandran map). Furthermore, spin diffusion correction permits the use of tighter error bounds which improves the distinction between signal and noise in an automated NOE assignment scheme.     

Analysis of Spin Diffusion and Cross Correlation on the Net Nuclear Overhauser Effect in NMR

The effect of dipole–dipole cross correlations on the net nuclear Overhauser effect (NOE) has been analyzed here for realistic systems by extending the three-spin calculations to four and five spins in order to account for additional cross correlations and spin diffusion. These have been compared with the addition of leakage terms to the three-spin system. The additional spins enhance cross-correlation effects on one hand but on the other act as supplementary relaxation pathways for the magnetization to diffuse. This analysis shows that for a linear array of spins in the long-correlation limit, dipole–dipole cross correlations increase net NOE, while spin diffusion decreases it, and that the cumulative effect is a reduced effect of cross correlations. In other geometries and correlation limits, the effect of cross correlations on net NOE is generally small.     

One-Dimensional NOE Experiments Using Pulsed Field Gradients

Previously, it has been shown that the use of pulsed field gradients in one-dimensional NOE experiments results in spectra of much higher quality than it has previously been possible to record. Such high-quality spectra make it possible to measure, with complete confidence, very small NOE enhancements and also make it straightforward to measure NOE buildup curves. In this paper, the spin dynamics behind these NOE experiments with gradients are analyzed in detail; the effects of strong coupling and molecular diffusion are also examined. It is also shown how the basic experiments can be improved upon, in particular how unwanted anti-phase contributions (SPT effects) can be eliminated entirely. Experimental illustrations of the various methods and improvements are given and practical recommendations made as to how the experiments are best performed.     

射频场强度对稳态核Overhauser效应增强的影响

通过分析在ＲＦ场照射下自旋体系的稳态特性，指出了区分稳态和饱和态的概念是非常必要的。用推广的Ｓｏｌｏｍｏｎ方程描述稳态ＮＯＥ实验，给出了稳态ＮＯＥ实验增强因子的修正表达式，并用实验证明了它的正确性。 关键词：     

Observation of long-range small-molecule NOEs using a neoteric sensitivity enhancement scheme.

A new method to increase the sensitivity of the 1D transient NOE experiment for molecules in the positive NOE regime is presented. This method, the reverse NOE, simply replaces the conventional relaxation delay between scans. Transient positive NOE enhancements from all other spins are used to accelerate the recovery of the target resonance toward its equilibrium intensity. In favorable cases, the intensity of the target peak at the start of an experiment can actually be increased beyond its equilibrium value. There is also a sensitivity enhancement in the rapid pulsing regime, where recovery is always incomplete. This sensitivity enhancement is illustrated with the one-dimensional double pulsed field gradient spin echo NOE experiment to observe a "fourth-order" NOE. Sensitivity gains of 30% are demonstrated.     

Versatility of the dipolar filter selection: from 1H nuclear spin diffusion experiment to the measurement of nuclear Overhauser effect in homopolymer melts

Dipolar filters select ¹H magnetization according to local dipolar dephasing, which corresponds to site mobility in systems with heterogeneous molecular mobility. Combined with a conventional exchange experiment, it is usually applied to polymeric samples exhibiting structures on the nanometer length scale associated with a strong dynamic contrast. There, the resulting ¹H nuclear spin diffusion experiment yields the size of the structure. When the same experiment is applied to homopolymer melts exhibiting a weak dynamic contrast and dynamic heterogeneities on significant shorter length scales, the recorded magnetization decay is in agreement with decays expected from a heterogeneous nanostructure. However, dipolar filters actually can also select mobile parts of the repeat unit, e.g. the end of the alkyl side chains and the subsequent magnetization transfer then can occur via cross relaxation due to non coherent zero-quantum transitions (nuclear Overhauser effect, NOE). The difficulties of distinguishing these two cases are examined and it is demonstrated that NOE experiments exploiting magnetization selection via the dipolar filter allow quantifying the local dynamics of the side chains. This opens new possibilities for measurements of local dynamics in non isotopically labeled homopolymer melts.     

Use of very long-distance NOEs in a fully deuterated protein: an approach for rapid protein fold determination

The high sensitivity of modern NMR instrumentation, in combination with full deuteration, enabled the measurement of long-range NOEs between amide protons in a fully deuterated protein corresponding to distances up to 8A. These are beyond the limit normally observed in protonated samples. Such long-distance NOEs could be observed using long mixing times, which became possible due to reduced spin diffusion and T1 relaxation of the amide protons in the fully deuterated sample. This information was used in combination with secondary structure restraints derived from secondary chemical shifts for structure calculations. With these backbone amide proton NOEs only, a unique fold could be obtained with positional root mean square deviations from the average of 1.30 and 2.25 A for backbone and heavy atoms, respectively. Despite the low density of restraints, no mirror image problems were observed. Addition of sidechain NOE information increased the precision of the ensemble and in particular of the core packing. The structures obtained in this way were close to the published crystal structure. NOE completeness analysis revealed that the cumulative completeness is still more than 80% for an 8.0 A cut-off distance.     

自旋密度光栅和本征GaAs量子阱中的电子自旋双极扩散

为研究空穴对自旋极化电子扩散的影响,提出用自旋密度光栅方法来观察电子自旋扩散过程。由飞秒激光在本征GaAs多量子阱中激发产生瞬态自旋光栅和瞬态自旋密度光栅,并用于研究电子自旋扩散和电子自旋双极扩散。实验测得自旋双极扩散系数Das ＝25.4 cm 2/s,低于自旋扩散系数Ds ＝113.0 cm 2/s,表明自旋密度光栅中电子自旋扩散受到空穴的显著影响。     

Dynamical NOE in multiple-spin systems undergoing chemical exchange

A relaxation-matrix procedure is given for the analysis of dynamical NOE of a multiple-spin system undergoing chemical exchange. It is demonstrated that, if fast exchange prevails, the evolution of the longitudinal magnetization of the spin system, summed over the exchanging species, is similar to that of a single nonexchanging species with a relaxation matrix given by the population-weighted average of the individual relaxation matrices. The complications generally involved in calculating the NOE for exchanging systems, stemming from the need to diagonalize large unsymmetrical matrices, are circumvented through the use of the average relaxation matrix which is real and symmetric and has the same dimension as the individual relaxation matrices.     

The reconstruction of the relaxation matrix from an incomplete set of nuclear overhauser effects

Internal motions in a macromolecule and indirect magnetization transfers (spin diffusion) prevent simple interpretation of NOE values in terms of structural and dynamic parameters in the course of the study of a macromolecule. A method for separating these two problems by first analyzing the NOES with respect to the relaxation rate constants is proposed. NOE values for 1 D or 2D experiments are obtained as nonlinear functions of the ϱ and σ parameters by solving the Bloch equations. A general least-squares minimization routine that makes use of the Hessian matrix of second derivatives was found to be efficient in determining iteratively the set of parameters that statistically correlates the corresponding calculated NOEs to a set of experimental NOES. The procedure was applied to probe the internal mobility of the deoxyriboses in a self-complementary hexamer, d(CGTACG)₂. It was found that H_2′-H_2″ and H_1′-H_2″-vectors are subject to internal motions whose amplitudes vary as we move along the sequence.     

本征GaAs量子阱中电子自旋扩散输运的时-空分辨吸收光谱研究

发展了一种时-空分辨圆偏振光抽运-探测光谱及其理论,并用于本征GaAs量子阱中电子自旋扩散输运的实验研究.获得室温下本征GaAs量子阱中的“自旋双极扩散系数”为D_as=37.5±15 cm²/s.此结果比用自旋光栅法测量到的掺杂GaAs量子阱中电子自旋扩散系数小.解释为是由于“空穴库仑拖曳”效应减慢了电子自旋波包的扩散输运. 关键词： 时-空分辨抽运-探测光谱 电子自旋扩散 GaAs量子阱     

在CP MAS NMR中测量质子自旋扩散速率的方法

自旋扩散在固体核磁共振的许多现象中都起着非常重要的作用。现有几种理论方案以估算扩散系数。然而在实践中这种估算既不实际也不可靠。本文提出了确定自旋扩散速率的新方案,它利用的是CP MAS NMR中的稀核退极化规律。带质子的稀核磁化矢量在退极化中表现出两个阶段,慢衰减的第二阶段是单一指数过程,它提供了自旋扩散速率的直接度量。自旋扩散实质上是极化转移的一种宏观表现形式,这种转移通过一系列成对自旋的flip-flop进行,可以用一维随机走步模型描述。从退磁过程半对数曲线的斜率可以求得平均flip-flop时间。自旋扩散系数可以由此估算。在一些典型的刚性有机固体和结晶高分子聚合物中,求得平均flip-flop的时间是700微秒左右。它比偶极相关时间大一个数量级。这意味着,自旋扩散时间常数与自旋—自旋弛豫时间常数是很不相同的,虽然这两个相应过程虽密切相关的。由质子线宽估计自旋扩散系数是不可靠的。     

1,2-取代乙烯衍生物结构的核磁共振研究

该文对1,2-取代乙烯衍生物的化学结构的NMR测定方法进行了研究. 结果表明,多频率位移激发双梯度自旋回波1D NOE新方法用于阐明这类化合物的化学结构具有独到之处. 强偶合自旋体系信号的选择性粒子数转移 (SPT)影响可得到有效抑制,NOE信号为吸收型,微小(约0.8%)的NOE信号也可明确测定,重叠复杂的谱峰可分离和辨认,测定顺反异构体不需要标准样品对照,结果准确、可靠. 该文以2-甲氧基-4-(2-苯基-2-环己基氨基甲酰基-乙烯基)-乙酸苯酯为例,阐明1D NOE方法在1,2-取代乙烯衍生物的化学结构和立体化学研究中的应用.     

量子气体中的输运行为

输运测量是了解物质性质的一个重要手段.本文简单介绍最近在量子气体中实现的输运实验及其主要结论,包括在类似于介观物理器件中的Landauer输运和强相互作用费米气体中的自旋输运行为.我们着重讨论自旋动力学的特殊性以及其由于全同粒子相互作用所导致的特殊自旋扩散流的形式.     

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

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.     

Solid-state 13C and 1H spin diffusion NMR analyses of the microfibril structure for bacterial cellulose

To obtain further information about the cause for the rather large splitting of the C4 resonance line into the downfield (C4D) and upfield (C4U) lines in CP/MAS ¹³C NMR spectra for native cellulose, ¹³C and ¹H spin diffusion measurements have been conducted by using different types of bacterial cellulose samples. In ¹³C spin diffusion measurements, the C4D resonance line is selectively inverted by the Dante π pulse sequence and the ¹³C spin diffusion is allowed to proceed from the C4D carbons to other carbons including the C4U carbons with use of the ¹³C4-enriched bacterial cellulose sample. The analysis based on the simple spin diffusion theory for the process experimentally observed reveals that the C4U carbons may be located at distances less than about 1 nm from the C4D carbons. In ¹H spin diffusion measurements, poly(vinyl alcohol) (PVA) films in which ribbon assemblies of bacterial cellulose are dispersed are employed and the ¹H spin diffusion process is examined from the water-swollen PVA continuous phase to the dispersed ribbon assemblies by the ¹³C detection through the ¹H–¹³C CP technique. As a result, it is found that the C4D and C4U carbons are almost equally subjected to the ¹H spin diffusion from the PVA phase, indicating that the C4U carbons are not localized in some limited area, e.g. in the surfacial region, but are distributed in the whole area in the microfibrils. These experimental results suggest that the C4U carbons may exist as structural defects probably due to conformational irregularity associated with disordered hydrogen bonding of the CH₂OH groups in the microfibrils.     

Spin dynamics in conducting polymers studied by μSR

We report studies of spin dynamics in the conducting polymers polyaniline and polypyrrole using both μ⁺SR and μ^-SR techniques. These measurements reveal characteristic field dependences and cutoff frequencies for the muon spin relaxation which can be related to the spin diffusion process. Clear evidence is seen for increased spin localisation at low temperatures where a crossover occurs from two or three dimensional spin diffusion to a one dimensional diffusion regime. This revised version was published online in August 2006 with corrections to the Cover Date.     

Transient NOE-exchange-relay experiment: application to ligand-protein binding under slow exchange conditions

A new version of one-dimensional (1)H experiment has been developed to probe ligand binding to macromolecular targets. The experiment, called transient NOE-exchange relay, is similar to the 'reverse NOE pumping' technique [A. Chen, M.J. Shapiro, J. Am. Chem. Soc. 122 (2000) 414-415]. The T(2) filter is used to erase protein magnetization, and the saturation then spreads from protein to bound ligand (via NOE) and further to a free ligand (via on-off exchange). The ligand signals, monitored as a function of mixing time, present a familiar 'dip' pattern characteristic of transient NOE or transient exchange experiments. In addition to the T(2) filter, we have also implemented a T(1) filter which makes use of the fact that the selective T(1)(-1) rates in macromolecules are much higher than those in small ligands. To model the experiment, complete relaxation and exchange matrix analysis has been invoked. This formalism was further used as a starting point to develop a simplified treatment where the relaxation and exchange components are represented by 2x2 matrix and, in addition, there is a special term responsible for coupling of ligand magnetization to the protein spin bath. The proposed experimental scheme has been tested on a system of peanut agglutinin complexed with Me-beta-D-galactopyranoside, which is known to be in a slow exchange regime. The results suggest that the NOE-exchange-relay experiment can be used at the advanced stages of the drug development process to confirm high-affinity ligand binding.     

Optical measurement and control of spin diffusion in n-doped GaAs quantum wells

Transient spin gratings are used to study spin diffusion in lightly n-doped GaAs quantum wells at low temperatures. The spin grating is shown to form in the excess electrons from doping, providing spin relaxation and transport properties of the carriers most relevant to spintronic applications. We demonstrate that spin diffusion of the these carriers is accelerated by increasing the density or energy of the optically excited carriers. These results can be used to better understand and even control spin transport in experiments that optically excite spin-polarized carriers.