Progress in Nuclear Magnetic Resonance Spectroscopy最新文献

In-cell NMR spectroscopy of nucleic acids: Basic concepts, practical aspects, and applications

IF 7.3 2区化学 Q2 CHEMISTRY, PHYSICAL

Progress in Nuclear Magnetic Resonance Spectroscopy

Pub Date : 2025-02-24 DOI: 10.1016/j.pnmrs.2025.101560

Silvie Foldynova-Trantirkova , Jakub Harnos , Jan Rynes , Vladimira Zlinska , Lukas Trantirek

In-cell NMR spectroscopy has recently emerged as a unique source of atomically resolved information on the structure, dynamics, and interactions of nucleic acids (NAs) within the intracellular space of living cells. Its recent applications have helped reveal fundamental differences in the behaviour of NAs in cells compared to the in vitro conditions commonly used for their study, as well as in physiologically distinct cellular states. This review covers the fundamental principles and practical aspects of acquiring in-cell NMR data in currently established eukaryotic cellular models, Xenopus laevis oocytes, and human cells. The primary purpose of this review is to present and discuss the technical and conceptual aspects of in-cell NMR sample preparations and their manipulations during in-cell NMR data acquisition, as understanding these aspects is vital for comprehending the physiological significance of in-cell NMR data and the information they provide. Considerations on the planning of in-cell NMR experiments and the presentation of in-cell NMR data on nucleic acids are discussed. We hope this will enable readers to navigate through the ever-growing pool of in-cell NMR literature and gain the knowledge needed to assess and comprehend published data independently. Additionally, we hope it will inspire some readers to actively participate in this rapidly expanding and fascinating field of cellular structural biology.

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引用次数: 0

Cardiovascular magnetic resonance imaging: Principles and advanced techniques

IF 7.3 2区化学 Q2 CHEMISTRY, PHYSICAL

Progress in Nuclear Magnetic Resonance Spectroscopy

Pub Date : 2025-02-24 DOI: 10.1016/j.pnmrs.2025.101561

Dongyue Si , Simon J. Littlewood , Michael G. Crabb , Andrew Phair , Claudia Prieto , René M. Botnar

Cardiovascular magnetic resonance (CMR) imaging is an established non-invasive tool for the assessment of cardiovascular diseases, which are the leading cause of death globally. CMR provides dynamic and static multi-contrast and multi-parametric images, including cine for functional evaluation, contrast-enhanced imaging and parametric mapping for tissue characterization, and MR angiography for the assessment of the aortic, coronary and pulmonary circulation. However, clinical CMR imaging sequences still have some limitations such as the requirement for multiple breath-holds, incomplete spatial coverage, complex planning and acquisition, low scan efficiency and long scan times. To address these challenges, novel techniques have been developed during the last two decades, focusing on automated planning and acquisition timing, improved respiratory and cardiac motion handling strategies, image acceleration algorithms employing undersampled reconstruction, all-in-one imaging techniques that can acquire multiple contrast/parameters in a single scan, deep learning based methods applied along the entire CMR imaging pipeline, as well as imaging at high- and low-field strengths. In this article, we aim to provide a comprehensive review of CMR imaging, covering both established and emerging techniques, to give an overview of the present and future applications of CMR.

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引用次数: 0

Zero- to ultralow-field nuclear magnetic resonance

IF 7.3 2区化学 Q2 CHEMISTRY, PHYSICAL

Progress in Nuclear Magnetic Resonance Spectroscopy

Pub Date : 2025-02-15 DOI: 10.1016/j.pnmrs.2025.101558

Danila A. Barskiy , John W. Blanchard , Dmitry Budker , James Eills , Szymon Pustelny , Kirill F. Sheberstov , Michael C.D. Tayler , Andreas H. Trabesinger

Zero and ultralow-field nuclear magnetic resonance (ZULF NMR) is an NMR modality where experiments are performed in fields at which spin–spin interactions within molecules and materials are stronger than Zeeman interactions. This typically occurs at external fields of microtesla strength or below, considerably smaller than Earth’s field. In ZULF NMR, the measurement of spin–spin couplings and spin relaxation rates provides a nondestructive means for identifying chemicals and chemical fragments, and for conducting sample or process analyses. The absence of the symmetry imposed by a strong external magnetic field enables experiments that exploit terms in the nuclear spin Hamiltonian that are suppressed in high-field NMR, which in turn opens up new capabilities in a broad range of fields, from the search for dark matter to the preparation of hyperpolarized contrast agents for clinical imaging. Furthermore, as in ZULF NMR the Larmor frequencies are typically in the audio band, the nuclear spins can be manipulated with d.c. magnetic field pulses, and highly sensitive magnetometers are used for detection. In contrast to high-field NMR, the low-frequency signals readily pass through conductive materials such as metals, and heterogeneous samples do not lead to resonance line broadening, meaning that high-resolution spectroscopy is possible. Notable practical advantages of ZULF NMR spectroscopy are the low cost and relative simplicity and portability of the spectrometer system. In recent years ZULF NMR has become more accessible, thanks to improvements in magnetometer sensitivity and commercial availability, and the development of hyperpolarization methods that provide a simple means to boost signal strengths by several orders of magnitude. These topics are reviewed and a perspective on potential future avenues of ZULF-NMR research is presented.

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引用次数: 0

Principles and Progress in ultrafast 2D spatiotemporally encoded MRI

IF 7.3 2区化学 Q2 CHEMISTRY, PHYSICAL

Progress in Nuclear Magnetic Resonance Spectroscopy

Pub Date : 2025-02-13 DOI: 10.1016/j.pnmrs.2025.101559

Mārtiņš Otikovs , Zhiyong Zhang , Lucio Frydman

Magnetic resonance imaging (MRI) is an indispensable tool used in both the lab and the clinic. Part of the strength of MRI comes from its ability to deliver anatomical information highlighted with different types of contrasts, including functional and diffusion-oriented acquisitions that are often incompatible with normal, multi-shot scans. For these problems, Nobel-award-winning techniques such as Echo Planar Imaging (EPI) have been essential in opening a manifold of new applications. EPI, however, has challenges when dealing with sharp changes in magnetic susceptibility, including those arising in the presence of air/tissue or air/fat interfaces, from non-ferromagnetic metal implants, as well when the main magnetic field cannot be shimmed to achieve the desired degree of homogeneity, as often is the case in systems built using permanent magnets. Among the techniques being proposed to deal with this kind of problem is spatiotemporally-encoded (SPEN) MRI. The present review focuses on the principles of this technique, with an emphasis on: i) explaining SPEN's resilience to field inhomogeneities, on the basis of expanded bandwidth considerations vis-à-vis EPI; ii) “the good, the bad and the ugly” associated with the undersampling that SPEN usually has to carry out when employing expanded bandwidths; iii) recent developments in data processing algorithms seeking to alleviate the “bad and the ugly” part of these experiments by formulating SPEN image reconstruction as an optimization problem, and then relying on compressed sensing and parallel imaging concepts to achieve improved image quality; and iv) the incorporation of experimental improvements including scan interleaving, simultaneous multi-banding and multi-echo elements, to keep in line with advancements in other areas of fast MRI. The strengths and weaknesses of these data sampling and processing strategies are assessed, and examples of their leverage in functional, but foremost diffusion-weighted, imaging applications, are presented.

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引用次数: 0

Deep learning and its applications in nuclear magnetic resonance spectroscopy 深度学习及其在核磁共振波谱学中的应用

IF 7.3 2区化学 Q2 CHEMISTRY, PHYSICAL

Progress in Nuclear Magnetic Resonance Spectroscopy

Pub Date : 2025-01-17 DOI: 10.1016/j.pnmrs.2024.101556

Yao Luo, Xiaoxu Zheng, Mengjie Qiu, Yaoping Gou, Zhengxian Yang, Xiaobo Qu, Zhong Chen, Yanqin Lin

Nuclear Magnetic Resonance (NMR), as an advanced technology, has widespread applications in various fields like chemistry, biology, and medicine. However, issues such as long acquisition times for multidimensional spectra and low sensitivity limit the broader application of NMR. Traditional algorithms aim to address these issues but have limitations in speed and accuracy. Deep Learning (DL), a branch of Artificial Intelligence (AI) technology, has shown remarkable success in many fields including NMR. This paper presents an overview of the basics of DL and current applications of DL in NMR, highlights existing challenges, and suggests potential directions for improvement.

核磁共振作为一项先进的技术，在化学、生物、医学等各个领域有着广泛的应用。然而，多维光谱采集时间长、灵敏度低等问题限制了核磁共振的广泛应用。传统算法旨在解决这些问题，但在速度和准确性方面存在局限性。深度学习（DL）是人工智能（AI）技术的一个分支，在包括核磁共振在内的许多领域都取得了显著的成功。本文概述了深度学习的基础知识和目前深度学习在核磁共振中的应用，强调了存在的挑战，并提出了潜在的改进方向。

引用次数: 0

Nonlinear effects in magnetic resonance localized spectroscopy and images

IF 7.3 2区化学 Q2 CHEMISTRY, PHYSICAL

Progress in Nuclear Magnetic Resonance Spectroscopy

Pub Date : 2025-01-17 DOI: 10.1016/j.pnmrs.2025.101557

Dan Eugen Demco , Ana-Maria Oros-Peusquens , Nadim Jon Shah

The nonlinear effects associated with intermolecular multiple-quantum coherences (iMQCs) that are present in magnetic resonance imaging (MRI), localized spectroscopy (MRS), and spatially resolved thermometry of biological tissues are reviewed. These nonlinear effects occur especially for samples with a high concentration of resonant nuclei, at ultra-high magnetic fields or under hyperpolarization conditions. The classical Bloch equations and approaches based on quantum mechanical density operator evolution were employed for description of nonlinear effects on the spin system response in the presence of distant (long-range) dipolar field in samples containing high molecular mobility like liquids. The multiple spin echoes that appear in the presence of dipolar demagnetization fields in the presence of homogenous and heterogenous spin interactions and their applications are also discussed. One emphasis of the review is on the excitation, evolution, and detection of intermolecular zero-quantum coherences (iZQCs) and intermolecular double-quantum coherences (iDQCs) in the presence of correlated field gradients that represent the basis for CRAZED pulse sequences (Warren et al. Science 262 (1993) 2005–2009). The physics behind these methods employed for magnetically equivalent and non-equivalent spins, J-coupled spin, in homonuclear and heteronuclear systems is discussed. The principles of magnetic resonance localized spectroscopy and imaging applications for brain investigations to reduce the effect of inhomogeneous magnetic fields and to increase the image resolution is reviewed. The physics related to the used of CRAZED methods to produce fundamentally different contrast than does conventional imaging is also addressed. Collective effects in the presence of strong nuclear magnetization that can affect MRI and MRS results such as spectral clustering and spin turbulence are summarized.

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引用次数: 0

Hyperpolarised benchtop NMR spectroscopy for analytical applications 用于分析应用的超极化台式 NMR 光谱仪

IF 7.3 2区化学 Q2 CHEMISTRY, PHYSICAL

Progress in Nuclear Magnetic Resonance Spectroscopy

Pub Date : 2024-11-01 DOI: 10.1016/j.pnmrs.2024.10.001

Ana I. Silva Terra, Daniel A. Taylor, Meghan E. Halse

Benchtop NMR spectrometers, with moderate magnetic field strengths (

B_{0} = 1 - 2.4 T

) and sub-ppm chemical shift resolution, are an affordable and portable alternative to standard laboratory NMR (

B_{0} \geq 7 T

). However, in moving to lower magnetic field instruments, sensitivity and chemical shift resolution are significantly reduced. The sensitivity limitation can be overcome by using hyperpolarisation to boost benchtop NMR signals by orders of magnitude. Of the wide range of hyperpolarisation methods currently available, dynamic nuclear polarisation (DNP), parahydrogen-induced polarisation (PHIP) and photochemically-induced dynamic nuclear polarisation (photo-CIDNP) have, to date, shown the most promise for integration with benchtop NMR for analytical applications. In this review we provide a summary of the theory of each of these techniques and discuss examples of how they have been integrated with benchtop NMR detection. Progress towards the use of hyperpolarised benchtop NMR for analytical applications, ranging from reaction monitoring to probing biomolecular interactions, is discussed, along with perspectives for the future.

台式 NMR 光谱仪具有中等磁场强度（B0=1-2.4T）和亚ppm 级的化学位移分辨率，是标准实验室 NMR（B0≥7T）的经济实惠且便携的替代品。然而，在转用低磁场仪器时，灵敏度和化学位移分辨率会显著降低。使用超极化技术可将台式 NMR 信号提高几个数量级，从而克服灵敏度限制。在目前可用的各种超极化方法中，动态核极化 (DNP)、对氢诱导极化 (PHIP) 和光化学诱导动态核极化 (photo-CIDNP) 是迄今为止最有希望与台式 NMR 集成用于分析应用的方法。在本综述中，我们总结了每种技术的理论，并讨论了如何将这些技术与台式 NMR 检测相结合的实例。我们讨论了将超极化台式 NMR 用于分析应用（从反应监测到生物分子相互作用探测）的进展，以及对未来的展望。

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引用次数: 0

NMR investigations of glycan conformation, dynamics, and interactions 对聚糖构象、动力学和相互作用的核磁共振研究

IF 7.3 2区化学 Q2 CHEMISTRY, PHYSICAL

Progress in Nuclear Magnetic Resonance Spectroscopy

Pub Date : 2024-10-12 DOI: 10.1016/j.pnmrs.2024.10.002

Jesús Angulo , Ana Ardá , Sara Bertuzzi , Angeles Canales , June Ereño-Orbea , Ana Gimeno , Marcos Gomez-Redondo , Juan C. Muñoz-García , Paola Oquist , Serena Monaco , Ana Poveda , Luca Unione , Jesús Jiménez-Barbero

Glycans are ubiquitous in nature, decorating our cells and serving as the initial points of contact with any visiting entities. These glycan interactions are fundamental to host-pathogen recognition and are related to various diseases, including inflammation and cancer. Therefore, understanding the conformations and dynamics of glycans, as well as the key features that regulate their interactions with proteins, is crucial for designing new therapeutics. Due to the intrinsic flexibility of glycans, NMR is an essential tool for unravelling these properties. In this review, we describe the key NMR parameters that can be extracted from the different experiments, and which allow us to deduce the necessary geometry and molecular motion information, with a special emphasis on assessing the internal motions of the glycosidic linkages. We specifically address the NMR peculiarities of various natural glycans, from histo-blood group antigens to glycosaminoglycans, and also consider the special characteristics of their synthetic analogues (glycomimetics). Finally, we discuss the application of NMR protocols to study glycan-related molecular recognition events, both from the carbohydrate and receptor perspectives, including the use of stable isotopes and paramagnetic NMR methods to overcome the inherent degeneracy of glycan chemical shifts.

糖类在自然界中无处不在，它们装饰着我们的细胞，是与任何来访实体的最初接触点。这些聚糖相互作用是宿主-病原体识别的基础，并与包括炎症和癌症在内的各种疾病有关。因此，了解聚糖的构象和动态，以及调节其与蛋白质相互作用的关键特征，对于设计新疗法至关重要。由于聚糖固有的灵活性，核磁共振是揭示这些特性的重要工具。在这篇综述中，我们介绍了可从不同实验中提取的关键 NMR 参数，这些参数使我们能够推导出必要的几何和分子运动信息，尤其侧重于评估糖苷键的内部运动。我们特别讨论了从组织血型抗原到糖胺聚糖等各种天然聚糖的 NMR 特性，还考虑了它们的合成类似物（glycomimetics）的特殊性。最后，我们将从碳水化合物和受体的角度讨论应用核磁共振协议研究与聚糖相关的分子识别事件，包括使用稳定同位素和顺磁核磁共振方法克服聚糖化学位移的固有变性。

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引用次数: 0

NMR studies of amyloid interactions 淀粉样蛋白相互作用的核磁共振研究

IF 7.3 2区化学 Q2 CHEMISTRY, PHYSICAL

Progress in Nuclear Magnetic Resonance Spectroscopy

Pub Date : 2024-07-24 DOI: 10.1016/j.pnmrs.2024.07.001

David A. Middleton

Amyloid fibrils are insoluble, fibrous nanostructures that accumulate extracellularly in biological tissue during the progression of several human disorders, including Alzheimer’s disease (AD) and type 2 diabetes. Fibrils are assembled from protein monomers via the transient formation of soluble, cytotoxic oligomers, and have a common molecular architecture consisting of a spinal core of hydrogen-bonded protein β-strands. For the past 25 years, NMR spectroscopy has been at the forefront of research into the structure and assembly mechanisms of amyloid aggregates. Until the recent boom in fibril structure analysis by cryo-electron microscopy, solid-state NMR was unrivalled in its ability to provide atomic-level models of amyloid fibril architecture. Solution-state NMR has also provided complementary information on the early stages in the amyloid assembly mechanism. Now, both NMR modalities are proving to be valuable in unravelling the complex interactions between amyloid species and a diverse range of physiological metal ions, molecules and surfaces that influence the assembly pathway, kinetics, morphology and clearance in vivo. Here, an overview is presented of the main applications of solid-state and solution-state NMR for studying the interactions between amyloid proteins and biomembranes, glycosaminoglycan polysaccharides, metal ions, polyphenols, synthetic therapeutics and diagnostics. Key NMR methodology is reviewed along with examples of how to overcome the challenges of detecting interactions with aggregating proteins. The review heralds this new role for NMR in providing a comprehensive and pathologically-relevant view of the interactions between protein and non-protein components of amyloid. Coverage of both solid- and solution-state NMR methods and applications herein will be informative and valuable to the broad communities that are interested in amyloid proteins.

淀粉样纤维是一种不溶解的纤维状纳米结构，在阿尔茨海默病（AD）和 2 型糖尿病等几种人类疾病的发展过程中，会在生物组织的细胞外积聚。纤丝是由蛋白质单体通过瞬时形成的可溶性细胞毒性低聚物组装而成的，其共同的分子结构是由氢键连接的蛋白质β-链组成的脊髓核心。在过去的 25 年中，核磁共振光谱一直是研究淀粉样蛋白聚集体结构和组装机制的前沿领域。在冷冻电子显微镜对纤维结构进行分析的热潮兴起之前，固态核磁共振在提供淀粉样蛋白纤维结构的原子级模型方面一直是无与伦比的。溶液态 NMR 也为淀粉样蛋白组装机制的早期阶段提供了补充信息。现在，这两种 NMR 模式都被证明在揭示淀粉样蛋白物种与各种生理金属离子、分子和表面之间复杂的相互作用方面具有重要价值，这些相互作用影响着组装途径、动力学、形态和体内清除。本文概述了固态和溶液态 NMR 在研究淀粉样蛋白与生物膜、糖胺聚糖多糖、金属离子、多酚、合成疗法和诊断之间相互作用方面的主要应用。文章回顾了关键的核磁共振方法，并举例说明了如何克服检测聚集蛋白相互作用的挑战。这篇综述预示着 NMR 在提供淀粉样蛋白的蛋白质和非蛋白质成分之间相互作用的全面、病理相关视角方面的新作用。本文对固态和溶液态 NMR 方法和应用的论述将为对淀粉样蛋白感兴趣的各界人士提供丰富的信息和价值。

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引用次数: 0

The utility of small nutation angle 1H pulses for NMR studies of methyl-containing side-chain dynamics in proteins 小倾角 1H 脉冲在蛋白质含甲基侧链动态核磁共振研究中的应用

IF 6.1 2区化学 Q2 CHEMISTRY, PHYSICAL

Progress in Nuclear Magnetic Resonance Spectroscopy

Pub Date : 2024-06-06 DOI: 10.1016/j.pnmrs.2024.05.004

Vitali Tugarinov, G. Marius Clore

We describe the utility of small nutation angle (acute; <90°) ¹H radiofrequency pulses for efficient manipulation of magnetization in selectively [¹³CH₃]-labeled methyl groups of otherwise deuterated proteins. Focusing primarily on NMR applications that target either fast (pico-to-nanosecond) motions of the methyl group three-fold rotation axis, or slow (micro-to-millisecond) processes associated with chemical exchange, we show that significant simplification of the ¹³CH₃ spin-system and, as a consequence, of NMR pulse schemes, may be achieved in certain cases by the proper choice of the flip-angle of the ¹H acute-angle pulse. In other instances, appropriate adjustment of acute-angle ¹H pulses permits optimization of the sensitivity of NMR experiments. The results of acute-angle pulse based NMR experiments are validated by comparison with well-established NMR techniques for the characterization of fast dynamics of methyl-containing side-chains and chemical exchange processes.

我们介绍了小倾角（锐角；<90°）1H 射频脉冲在选择性[13CH3]标记的氚化蛋白质甲基中有效操纵磁化的实用性。我们主要侧重于针对甲基基团三倍旋转轴的快速（皮秒到纳秒）运动或与化学交换相关的慢速（微秒到毫秒）过程的核磁共振应用，我们的研究表明，在某些情况下，通过适当选择 1H 锐角脉冲的翻转角度，可以大大简化 13CH3 自旋系统以及核磁共振脉冲方案。在其他情况下，适当调整 1H 锐角脉冲可优化 NMR 实验的灵敏度。将基于锐角脉冲的核磁共振实验结果与用于表征含甲基侧链快速动力学和化学交换过程的成熟核磁共振技术进行比较，验证了这一结果。

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引用次数: 0