Efficient methods for obtaining phase-sensitive gradient-enhanced HMQC spectra

Summary Three improved versions of the gradient-enhanced HMQC experiment are presented which yield phase-sensitive spectra with increased sensitivity compared to the recently described field-gradient HMQC schemes. The first method uses a complex linear back-prediction in order to generate the FIDs at the t₁=0. With this approach, refocusing pulses on the heteronucleus are not necessary. The sequence is especially useful for larger proteins with short relaxation times for the coherences that evolve during t₁. In the other two methods lower and shorter gradient pulses or asymmetric gradients are used to optimize sensitivity.     

Potentials of radio-frequency field gradient NMR microscopy in environmental science

An understanding of transport, flow, diffusivity and mass transfer processes is of central importance in many fields of environmental biotechnology such as biofilm, bioreactor and membrane engineering, soil and groundwater bioremediation, and wastewater treatment. Owing to its remarkable sensitivity to molecular displacements and to its noninvasive and nondestructive character, pulsed field gradient (PFG) nuclear magnetic resonance (NMR) can be a valuable tool for investigating such processes. In conventional NMR microscopy, spatial encoding is achieved by using static magnetic field gradients (B ₀ gradients). However, an interesting alternative is to use radio-frequency magnetic field gradients (RF or B ₁ gradients). Although the latter are less versatile than the former, RF field gradient microscopy is particularly suitable for dealing with heterogeneous systems such as porous media because of its quasi-immunity to background static magnetic field gradients arising from magnetic susceptibility inhomogeneities, unlike the B ₀ gradients microscopy. Here, we present an overview of basic principles and the main features of this technique, which is still relatively unused. Different examples of diffusion imaging illustrate the potentialities of the method in both micro-imaging and the measurement of global or local diffusion coefficients within membranes and at liquid–solid interfaces. These examples suggest that a number of environmental problems could benefit from this technique. Different future prospects of application of B ₁ gradient NMR microscopy in environmental biotechnology are considered. Journal of Industrial Microbiology & Biotechnology (2001) 26, 53–61. Received 09 February 2000/ Accepted in revised form 07 August 2000     

Refocusing revisited: An optimized,gradient-enhanced refocused HSQC and its applications in 2D and 3D NMR and in deuterium exchange experiments

Summary 2D ¹⁵N-¹H correlation spectra are ideal for measuring backbone amide populations to determine amide exchange protection factors in studies of protein folding or other structural features. Most protein NMR spectroscopists use HSQC, which has been shown to be generally superior to HMQC in both resolution and sensitivity. The refocused HSQC experiment is intrinsically less sensitive than the regular HSQC, due to T₂ relaxation during the refocusing delays. However, we show here that, when high ¹⁵N resolution is needed, an optimized refocused HSQC sequence that utilizes a semi-constant time evolution period and pulsed field gradients has better signal-to-noise ratio and resolution, and integrates more accurately, than a similar HSQC. The differences are demonstrated on a 20 kDa protein. The technique can also be applied to 3D NOESY experiments to eliminate strong NH₂ geminal peaks and their truncation artefacts at a modest cost in sensitivity.     

Robust refocusing of 13C magnetization in multidimensional NMR experiments by adiabatic fast passage pulses

We show that adiabatic fast passage (AFP) pulses are robust refocusing elements of transverse ¹³C magnetization in multidimensional NMR experiments. A pair of identical AFP pulses can refocus selected parts or a complete ¹³ C chemical shift range in ¹³C spectra. In the constant time ¹³C-¹H HSQC, replacement of attenuated rectangular pulses by selective AFP pulses results in a sensitivity enhancement of up to a factor of 1.8. In the 3D CBCA(CO)NH the signal-to-noise ratio is increased by a factor of up to 1.6.     

Minimisation of sensitivity losses due to the use of gradient pulses in triple-resonance NMR of proteins

Summary The use of pulsed field gradients in multiple-pulse NMR experiments has many advantages, including the possibility of obtaining excellent water suppression without the need for selective presaturation. In such gradient experiments the water magnetization is dephased deliberately; exchange between the saturated protons of the solvent water and the NH protons of a protein transfers this saturation to the protein. As the solvent is in large excess and relaxes relatively slowly, the result is a reduction in the sensitivity of the experiment due to the fact that the NH proton magnetization is only partially recovered. These effects can be avoided by ensuring that the water magnetization remains intact and is returned to the +z-axis at the start of data acquisition. General procedures for achieving this aim in any triple-resonance experiment are outlined and two specific examples are given. Experimental results confirm the sensitivity advantage of the modified sequences.     

New pulsed field gradient NMR experiments for the detection of bound water in proteins

Summary New H₂O-selective homonuclear and heteronuclear 2D NMR experiments have been designed for the observation of protein hydration (PHOGSY, Protein Hydration Observed by Gradient Spectroscop Y). These experiments utilize selective excitation of the H₂O resonance and pulsed field gradients for coherence selection and efficient H₂O suppression. The method allows for a rapid and sensitive detection of H₂O molecules in labelled and unlabelled proteins. In addition it opens a way to measure the residence time of water bound to proteins. Its application to uniformly ¹⁵N-labelled FKBP-12 (FK-506 binding protein) is demonstrated.     

QSim, a program for NMR simulations

We present QSim, a program for simulation of NMR experiments. Pulse sequences are implemented and analyzed in QSim using a mouse driven interface. QSim can handle almost any modern NMR experiment, using multiple channels, shaped pulses, mixing, decoupling, phase-cycling and pulsed field gradients. Any number of spins with any spin quantum number can, in theory, be used in simulations. Relaxation is accounted for during all steps of pulse sequences and relaxation interference effects are supported. Chemical kinetics between any numbers of states can be simulated. Both classical and quantum mechanical calculations can be performed. The result of a simulation can be presented either as magnetization as a function of time or as a processed spectrum.     

Real-time pure shift <Superscript>15</Superscript>N HSQC of proteins: a real improvement in resolution and sensitivity

Spectral resolution in proton NMR spectroscopy is reduced by the splitting of resonances into multiplets due to the effect of homonuclear scalar couplings. Although these effects are often hidden in protein NMR spectroscopy by low digital resolution and routine apodization, behind the scenes homonuclear scalar couplings increase spectral overcrowding. The possibilities for biomolecular NMR offered by new pure shift NMR methods are illustrated here. Both resolution and sensitivity are improved, without any increase in experiment time. In these experiments, free induction decays are collected in short bursts of data acquisition, with durations short on the timescale of J-evolution, interspersed with suitable refocusing elements. The net effect is real-time (t ₂) broadband homodecoupling, suppressing the multiplet structure caused by proton–proton interactions. The key feature of the refocusing elements is that they discriminate between the resonances of active (observed) and passive (coupling partner) spins. This can be achieved either by using band-selective refocusing or by the BIRD element, in both cases accompanied by a nonselective 180° proton pulse. The latter method selects the active spins based on their one-bond heteronuclear J-coupling to ¹⁵N, while the former selects a region of the ¹H spectrum. Several novel pure shift experiments are presented, and the improvements in resolution and sensitivity they provide are evaluated for representative samples: the N-terminal domain of PGK; ubiquitin; and two mutants of the small antifungal protein PAF. These new experiments, delivering improved sensitivity and resolution, have the potential to replace the current standard HSQC experiments.     

Rapid acquisition of three-dimensional triple-resonance experiments using pulsed field gradient techniques

Summary A rapid method for recording three-dimensional triple-resonance experiments utilising pulsed field gradient techniques is proposed, and applied to the HNCO experiment. In order to optimise the sensitivity of the method, a short phase cycle is used in conjunction with the pulsed field gradients to select the desired coherence transfer pathway. The method is demonstrated for the HU protein.     

Forest Remnants Along Urban-Rural Gradients: Examining Their Potential for Global Change Research

Over the next century, ecosystems throughout the world will be responding to rapid changes in climate and rising levels of carbon dioxide, inorganic N and ozone. Because people depend on biological systems for water, food and other ecosystem services, predicting the range of responses to global change for various ecosystem types in different geographic locations is a high priority. Modeling exercises and manipulative experimentation have been the principle approaches used to place upper and lower bounds on community and ecosystem responses. However, each of these approaches has recognized limitations. Manipulative experiments cannot vary all the relevant factors and are often performed at small spatio-temporal scales. Modeling is limited by data availability and by our knowledge of how current observations translate into future conditions. These weaknesses would improve if we could observe ecosystems that have already responded to global change factors and thus presage shifts in ecosystem structure and function. Here we consider whether urban forest remnants might offer this ability. As urban forests have been exposed to elevated temperature, carbon dioxide, nitrogen deposition and ozone for many decades, they may be ahead of the global change “response curve” for forests in their region. Therefore, not only might forests along urbanization gradients provide us with natural experiments for studying current responses to global change factors, but their legacy of response to past urbanization may also constitute space-for-time substitution experiments for predicting likely regional forest responses to continued environmental change. For this approach to be successful, appropriate criteria must be developed for selecting forest remnants and plots that would optimize our ability to detect incipient forest responses to spatial variation in global change factors along urbanization gradients, while minimizing artifacts associated with remnant size and factors other than those that simulate global change. Studying forests that meet such criteria along urban-to-rural gradients could become an informative part of a mixed strategy of approaches for improving forecasts of forest ecosystem change at the regional scale.     

An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates

Multidimensional NMR spectroscopy is a well-established technique for the characterization of structure and fast-time-scale dynamics of highly populated ground states of biological macromolecules. The investigation of short-lived excited states that are important for molecular folding, misfolding and function, however, remains a challenge for modern biomolecular NMR techniques. Off-equilibrium real-time kinetic NMR methods allow direct observation of conformational or chemical changes by following peak positions and intensities in a series of spectra recorded during a kinetic event. Because standard multidimensional NMR methods required to yield sufficient atom-resolution are intrinsically time-consuming, many interesting phenomena are excluded from real-time NMR analysis. Recently, spatially encoded ultrafast 2D NMR techniques have been proposed that allow one to acquire a 2D NMR experiment within a single transient. In addition, when combined with the SOFAST technique, such ultrafast experiments can be repeated at high rates. One of the problems detected for such ultrafast protein NMR experiments is related to the heteronuclear decoupling during detection with interferences between the pulses and the oscillatory magnetic field gradients arising in this scheme. Here we present a method for improved ultrafast data acquisition yielding higher signal to noise and sharper lines in single-scan 2D NMR spectra. In combination with a fast-mixing device, the recording of ¹H–¹⁵N correlation spectra with repetition rates of up to a few Hertz becomes feasible, enabling real-time studies of protein kinetics occurring on time scales down to a few seconds.     

Cross-correlation suppressed T1 and NOE experiments for protein side-chain 13CH2 groups

Relaxation measurements of side-chain ¹³CH₂-groups of uniformly ¹³C labeled human ubiquitin were performed at 600 MHz and 800 MHz magnetic field strength at 30°C. Dipole-dipole cross-correlated relaxation effects in T₁ experiments were suppressed by the combination of radio-frequency pulses and pulsed field gradients during the relaxation delay leading to monoexponential relaxation decays that allow a more accurate extraction of the ¹³C T₁ relaxation times. Heteronuclear ¹H-¹³C NOEs obtained by using different proton saturation schemes indicate that the influence of cross-correlation is small. The experimental T₁ and NOE data were interpreted in a model-free way in terms of a generalized order parameter and an internal correlation time.     

Enhanced sensitivity of rapidly exchanging amide protons by improved phase cycling and the constructive use of radiation damping

Summary Two alternative, general methods are presented that lead to enhanced signal intensity of rapidly exchanging protons. Both methods work by avoiding saturation of the water resonance, and are convenient to implement since they do not use any selective pulses. One method carefully chooses proton pulse phases and gradient strength and position in such a way that the water is realigned along the +z axis at the beginning of the acquisition time. An alternative method is proposed for cases where the pulse sequence does not allow such phase cycling. The latter uses radiation damping to bring water back to the +z axis 20–30 ms after acquisition. The methods are applied to the triple-resonance experiments HNCA, HNCO and HN(CO)CA. Both methods require pulsed B₀ field gradients and can result in higher signal intensity by a factor of two or more.     

Roles of H2S in adaptation of alpine plants Lamiophlomis rotata to altitude gradients

Hydrogen sulfide (H₂S) is an important gaseous transmitter in organisims. It widespreads in the organs and tissues of animals and participates in the biological process of cardiovascular relaxation, cell apoptosis and protection, inflammation and neuromodulation. H₂S also can be synthesized in plants system and is involved in stress responses and the biological process of growth and development. This review describes the synthesis and biological function of H₂S in plants. Based on our research for the adaptation of Lamiophlomis rotata to different altitude gradients, we firstly proposed H₂S plays an important role in the adaptation of Lamiophlomis rotata to alpine environment.     

Characterization of the prostaglandin H2 mimic: binding to the purified human thromboxane A2 receptor in solution

For decades, the binding of prostaglandin H₂ (PGH₂) to multiple target proteins of unrelated protein structures which mediate diverse biological functions has remained a real mystery in the field of eicosanoid biology. Here, we report that the structure of a PGH₂ mimic, U46619, bound to the purified human TP, was determined and compared with that of its conformation bound to the COX-downstream synthases, prostacyclin synthase (PGIS) and thromboxane A₂ synthase (TXAS). Active human TP protein, glycosylated and in full length, was expressed in Sf-9 cells using a baculovirus (BV) expression system and then purified to near homogeneity. The binding of U46619 to the purified receptor in a nonionic detergent-mimicked lipid environment was characterized by high-resolution NMR spectroscopy. The conformational change of U46619, upon binding to the active TP, was evidenced by the significant perturbation of the chemical shifts of its protons at H3 and H4 in a concentration-dependent manner. The detailed conformational changes and 3D structure of U46619 from the free form to the TP-bound form were further solved by 2D ¹H NMR experiments using a transferred NOE (trNOE) technique. The distances between the protons of H11 and H18, H11 and H19, H15 and H18, and H15 and H19 in U46619 were shorter following their binding to the TP in solution, down to within 5 Å, which were different than that of the U46619 bound to PGIS and U44069 (another PGH₂ mimic) bound to TXAS. These shorter distances led to further separation of the U46619 α and ω chains, forming a unique “rectangular” shape. This enabled the molecule to fit into the ligand-binding site pocket of a TP model, in which homology modeling was used for the transmembrane (TM) domain, and NMR structures were used for the extramembrane loops. The proton perturbations and 3D conformations in the TP-bound U46619 were different with that of the PGH₂ mimics bound to PGIS and TXAS. The studies indicated that PGH₂ can adopt multiple conformations in solution to satisfy the specific and unique shapes to fit the different binding pockets in the TP receptor and COX-downstream enzymes. The results also provided sufficient information for speculating the molecular basis of how PGH₂ binds to multiple target proteins even though unrelated in their protein sequences.     

A study of protein-water exchange through the off-resonance ROESY experiment: Application to the DNA-binding domain of AlcR

Summary In this communication a new NMR experiment for the safe observation and quantification of water-protein exchange phenomena is presented. It combines a water-selective pulse, offering chemical shift-based separation, and the off-resonance ROESY dynamic filter, which permits the elimination of the unwanted intramolecular dipolar cross relaxation of protein protons. Moreover, pulsed field gradients are used for the suppression of radiation damping and the solvent signal. The straightforward incorporation of this sequence in heteronuclear experiments is demonstrated for the case of the DNA-binding domain of the alcohol regulator protein.     

Phase shifting by novelty-induced running: activity dose-response curves at different circadian times

This study compared phase shifting after novelty-induced running at different circadian times (CTs). In Experiment 1, hamsters were confined to novel wheels for 3 h, starting at CTs 2, 4, 6, 8, 10 or 22. The largest shifts were found at CTs 2, 4 and 6. At each CT there was a relationship between the number of revolutions during the pulse and the size of phase shift. Maximum shifts were usually observed at each CT when animals ran 5000–9000 revolutions during the pulse. In Experiment 2, hamsters were confined to novel wheels for 1 h, also starting at CTs 2, 4, 6, 8, 10 or 22. Unlike with 3-h pulses, the largest shifts with 1-h pulses occurred at CT 8. In Experiment 3, hamsters were shut into a small nest box after a 1-h pulse at CT 8; phase shifting was unaffected, showing that movement about the home cage after a 1-h pulse had ended was not required for shifting. At CTs 2, 4 and 22, 3-h pulses produced shifts but 1-h pulses did not. Possibly, there are two different mechanisms of nonphotic phase shifting that can be activated by being placed in a novel wheel, but the results can also be explained in terms of a single mechanism. Accepted: 8 August 1997     

医学领域的磁共振成像革命——2003年诺贝尔生理及医学奖主要工作介绍

在磁场中 ,自旋的原子核会吸收频率与其自旋频率相同的电磁波 ,使自身能量增加 ,发生能级跃迁 ,当原子核迁移回原能级时 ,就会把多余的能量以电磁波的形式释放出来 ,称为核磁共振 (NMR) .磁共振成像(MRI)利用这一原理 ,依据所释放的能量在物质内部不同结构环境中不同的衰减 ,通过外加梯度磁场检测所发射出的电磁波 ,即可得知构成这一物体原子核的位置和种类 ,据此可以绘制成物体内部的结构图像 .将这种技术用于人体内部结构的成像 ,就产生出一种革命性的医学诊断工具 .快速变化的梯度磁场的应用 ,大大加快了磁共振成像的速度 ,使该技术在临床诊断、科学研究的应用成为现实 ,极大地推动了医学、神经生理学和认知神经科学的迅速发展     

Influence of oxygen on sulfate reduction and growth of sulfate-reducing bacteria

The ambivalent relations of sulfate-reducing bacteria to molecular O₂ have been studied with ten freshwater and marine strains. Generally, O₂ was reduced prior to sulfur compounds and suppressed the reduction of sulfate, sulfite or thiosulfate to sulfide. Three strains slowly formed sulfide at O₂ concentrations of below 15 M (6% air saturation). In homogeneously aerated cultures, two out of seven strains tested, Desulfovibrio desulfuricans and Desulfobacterium autotrophicum, revealed weak growth with O₂ as electron acceptor (up to one doubling of protein). However, O₂ was concomitantly toxic. Depending on its concentration cell viability and motility decreased with time. In artificial oxygen-sulfide gradients with sulfide-containing agar medium and also in sulfide-free agar medium under an oxygen-containing gas phase, sulfate reducers grew in bands close to the oxic/anoxic interface. The specific O₂ tolerance and respiration capacity of different strains led to characteristically stratified gradients. The maximum O₂ concentration at the surface of a bacterial band (determined by means of microelectrodes) was 9 M. The specific rates of O₂ uptake per cell were in the same order of magnitude as the sulfate reduction rates in pure cultures. The bacteria stabilized the gradients, which were rapidly oxidized in the absence of cells or after killing the cells by formaldehyde. The motile strain Desulfovibrio desulfuricans CSN slowly migrated in the gradients in response to changing O₂ concentrations in the gas phase.     

Nuclear magnetic resonance chemical shifts of potassium ions (39K) on ion exchange resins and in muscle

Chemical shifts of potassium (39K) were calculated from frequencies of beat patterns measured by a pulsed NMR method. This method indicates large chemical shifts for 3 molar KNO3 and 6 molal KI in good quantitative agreement with the steady state NMR measurements of previous investigators. 39K on two wet ion exchange resins and 39K in fresh muscle show insignificant chemical shifts relative to 0.1 M KCl solution. Previous studies showed marked shortening of NMR relaxation times (T1 and T2) for 39K in ion exchange resins and in muscle compared to free solution. These results seem to indicate that even though potassium on resins and in muscle experiences high electric field gradients, these have relatively little effect on the chemical shift of potassium, which may be correlated with the low pK values of the anionic groups in the resins and muscle.