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Introduction: Biomolecular NMR Spectroscopy
Chemical Reviews ( IF 51.4 ) Pub Date : 2022-05-25 , DOI: 10.1021/acs.chemrev.2c00142
Angela M Gronenborn 1 , Tatyana Polenova 2
Affiliation  

This article is part of the Biomolecular NMR Spectroscopy special issue. Since the initial discovery of the magnetic resonance phenomenon in physics, NMR spectroscopy has evolved over the last 70 years, via widespread applications as an analytical tool in chemistry, into a versatile methodology that can address biological questions. This Thematic Issue on Biomolecular NMR Spectroscopy aims to bring recent advances into focus and highlights state-of-the-art methodological developments as well as pioneering applications in solution and in the solid state. All contributions showcase what we consider to be the best and the brightest science in this arena. We are pleased to share with the readership of Chemical Reviews contributions from the large, vibrant, and diverse biomolecular NMR community that has grown through decades worth of scholarship, expertise, and tradition, captivated by the conceptual beauty of magnetic resonance and the richness of its applications in all areas of contemporary biological chemistry, structural and chemical biology, biophysics, bioengineering, and drug discovery. Owing to exciting recent breakthroughs in magnet technologies and instrumentation hardware, pulse sequences, data acquisition and analysis, as well as sample preparation, unprecedented amounts of atomic-level information on the structure and dynamics of biological systems are becoming available. These advances have opened doors for addressing and answering questions with exceptional accuracy, reliability, and scope, not possible previously, by NMR or any other method. Furthermore, there is ample opportunity for optimism, especially considering advances in adjacent areas, such as machine learning and artificial intelligence as well as innovations in other synthetic and engineering methodologies in chemical biology. While it is impossible to represent a fully comprehensive survey of the entire field, this Thematic Issue of Chemical Reviews contains 17 in-depth accounts of different aspects of biomolecular NMR and its applications. Here, we briefly summarize the content of each review in compact form, loosely grouped into two categories: solution-state and solid-state NMR. Within each group, articles are ordered arbitrarily according to the last name of the senior authors. Nine articles cover topics in solution-state NMR. Banci and co-workers provide a detailed overview of the development and applications of in-cell NMR during the 20 years after its initial launch. Existing approaches for the preparation of cellular samples and isotopic labeling strategies are reviewed, as well as the development of NMR bioreactor devices, allowing for real-time monitoring of intracellular metabolites and proteins. Bax and co-workers focus their contribution on the power of using weak alignment of biomolecules in solution and the measurement of residual dipolar couplings (RDCs). They review unique pulse schemes tailored to different types of RDCs and provide examples of how these structural parameters permit structure validation and refinement, de novo structure determination, as well as quantification of backbone and domain motions. Blackledge and co-workers summarize the distinctive capabilities of NMR to characterize intrinsically disordered proteins (IDPs) by providing ensemble averaged structural and dynamic parameters that describe the conformational energy landscape. Recent applications of NMR approaches to elucidate the nature and time scales of local and long-range dynamics in functional disordered assemblies are presented. In contrast to most other reviews in this issue that center on proteins, Dayie and co-workers discuss RNA molecules and how NMR is employed to investigate the structural dynamics of RNA in solution. They demonstrate how selective isotope labeling overcomes limitations imposed by large line widths, scalar and dipolar couplings, as well as spectral overlap, especially for big RNAs. Ingenious labeling techniques coupled with tailored pulse sequences provide a view into the important field of RNA structural biology. Hagn and co-workers review the benefits of using lipid nanodiscs for NMR structural investigations of membrane proteins in a physiologically relevant environment. A detailed overview of the currently available and popular lipid nanodisc systems is provided, including workflow optimization. Furthermore, a comprehensive description of the distinct advantages of such lipid systems for studying the structure, binding, interactions, and functional dynamics of membrane proteins is given. The amazing potential of exploiting the cross-talk between the magnetic moment of unpaired electrons and nuclear spins for structural purposes is illustrated by Hiller and co-workers. Large chemical shift changes mediated by paramagnetic centers in proteins, called pseudocontact shifts (PCS), are generated by these dipole–dipole interactions that are active over long distances (≥50 Å). Different tags for chelating lanthanoid ions are described as well as their uses in large biomolecular complexes and inside living cells. Pierattelli and co-workers present a suite of 13C-detected multinuclear experiments that provide unique information on proteins. The advantages of 13C over 1H detection are discussed, and important technical aspects that need to be taken into consideration are presented. In addition, instances where these types of experiments beautifully complement traditional proton spectra are highlighted. The emerging field of in-cell NMR for answering questions in structural biology is at the center of a review by Theillet and co-workers. The versatility and uniqueness of the atom-scale information provided by different nuclei are emphasized. Furthermore, a brief overview of the other main techniques in in-cell structural biology, such as EPR, smFRET, and cryo-ET, is presented, as well the relative advantages and disadvantages of in-cell NMR compared to these complementary approaches. Ubbink and co-workers provide a comprehensive overview centered on state-of-the-art paramagnetic tags used in bioNMR. Particular emphasis is placed on synthesis routes as well as their diverse chemical properties. The authors discuss in depth the pros and cons of specific tags for various applications. Uniquely, this contribution also describes paramagnetic tags designed specifically for structural studies of DNA and RNA by NMR and EPR spectroscopy. Eight reviews cover solid-state NMR methods for biological solids. Agarwal and co-workers introduce the reader to the methodological foundations of static and magic angle spinning (MAS) solid-state NMR spectroscopy relevant for state-of-the-art biological applications, with specific examples of protein structures solved by solid-state NMR. The comprehensive paper by Corzilius and co-workers focuses on the emerging field of dynamic nuclear polarization (DNP), presenting a review of mechanisms, polarizing agents, and the state-of-the-art applications of DNP-enhanced NMR to biological problems. Chow, De Paëpe, and Hediger present a comprehensive account of strategies and challenges in state-of-the-art DNP instrumentation, experimental protocols, and sample preparation, together with a broad range of applications into protein folding/misfolding/disorder, nucleic acids, viruses, membrane proteins, cell walls, and biomolecules in the cellular and extracellular context. Hong and co-workers present a powerful review of 19F- and 1H-based MAS NMR methods for correlation spectroscopy and distance measurements in biological systems, spanning proteins, nucleic acids, and carbohydrates, as well as their complexes and assemblies. Hou and co-workers review the current advances in dipolar and chemical shift recoupling methods by MAS NMR, presenting elegant applications for structural and dynamics studies of biomolecules. Pintacuda and co-workers discuss the emerging tour-de-force methodologies and applications of high-frequency MAS NMR that led to the “sensitivity and resolution revolution” in the field and opened doors to structural and dynamics analysis of challenging biological assemblies. The beautiful review by Reif describes the versatile use of deuteration and proton detection for high-resolution MAS NMR spectroscopy of biological systems, including labeling strategies and experimental approaches for resonance assignments and quantitative characterization of structure and dynamics. Wang and co-workers discuss state-of-the-art MAS NMR and DNP-enhanced MAS NMR techniques to study the structural organization and dynamic properties of the extracellular matrices and cell walls of algae, bacteria, fungi, and plants. They discuss unique insights that can be gained into these ubiquitous biomaterials inaccessible by other techniques. We warmly thank all the authors who submitted their reviews as promised and in time to be included in the printed version of this Thematic Issue and hope that the readers find them enjoyable, informative, and stimulating. Efforts by the Editorial Office of Chemical Reviews to usher the papers through the review process and assemble them into this issue are greatly appreciated. Angela M. Gronenborn is the UPMC Rosalind Franklin Professor and Chair of the Department of Structural Biology at the University of Pittsburgh, where she has been since 2005. She received a Ph.D. in Chemistry from the University of Cologne, Germany, in 1978. A major research thrust of her lab involves understanding how biological macromolecules work based on their structure and dynamics. Her group combines nuclear magnetic resonance (NMR) spectroscopy and other structural techniques with biophysics, biochemistry, and chemistry in an integrative fashion to investigate cellular processes at the molecular and atomic levels in relation to human disease. For her research contributions, she has been recognized by several awards, including the Mildred Cohen Award in Biological Chemistry, the Richard R. Ernst Prize in Magnetic Resonance, the E. Bright Wilson Award in Spectroscopy, and the Biophysical Society Founders Award. She has been elected to the National Academy of Sciences, the Norwegian Academy of Science and Letters, the German National Academy of Sciences, and the American Academy of Arts and Sciences. Tatyana Polenova is Professor of Chemistry and Biochemistry at the University of Delaware. She received her undergraduate degree (diploma with excellence) from Moscow State University in 1992. She received her Ph.D. degree from Columbia University in 1997, working in the laboratory of Professor Ann McDermott. After a postdoctoral position at Columbia, in 1999 she joined the faculty of City University of New York-Hunter College, and in 2003 she relocated to the University of Delaware. Her research focuses on solid-state NMR methods development and applications to understanding the structure, dynamics, and function of biological systems, including viral and cytoskeleton protein assemblies. Polenova is a Fellow of the International Society of Magnetic Resonance. She is the Editor in Chief of Journal of Magnetic Resonance, an Associate Developmental Editor of Journal of Structural Biology and Journal of Structural Biology: X, and an Associate Editor of Journal of Biomolecular NMR. This article has not yet been cited by other publications.

中文翻译:

简介:生物分子核磁共振光谱

本文是部分生物分子核磁共振光谱特刊。自从在物理学中最初发现磁共振现象以来,核磁共振波谱在过去 70 年中通过作为化学分析工具的广泛应用发展成为可以解决生物学问题的通用方法。本期生物分子核磁共振光谱专题旨在聚焦最新进展,重点介绍最先进的方法学发展以及在溶液和固态中的开创性应用。所有贡献都展示了我们认为是该领域最好和最聪明的科学。我们很高兴与《化学评论》的读者分享来自庞大、充满活力和多样化的生物分子 NMR 社区的贡献,该社区通过数十年的学术、专业知识和传统而发展壮大,被磁共振的概念之美及其在当代生物化学、结构和化学生物学、生物物理学、生物工程和药物发现。由于最近在磁体技术和仪器硬件、脉冲序列、数据采集和分析以及样品制备方面取得了令人兴奋的突破,有关生物系统结构和动力学的原子级信息量空前巨大。这些进步为解决和回答问题打开了大门,具有非凡的准确性、可靠性和范围,这在以前是不可能通过 NMR 或任何其他方法实现的。此外,还有很多乐观的机会,特别是考虑到相邻领域的进步,例如机器学习和人工智能,以及化学生物学中其他合成和工程方法的创新。虽然不可能对整个领域进行全面全面的调查,但本期化学评论包含 17 个关于生物分子核磁共振及其应用的不同方面的深入说明。在这里,我们以紧凑的形式简要总结每篇评论的内容,大致分为两类:溶液态和固态 NMR。在每个组中,文章根据资深作者的姓氏任意排序。九篇文章涵盖了溶液态 NMR 的主题。Banci 及其同事详细介绍了细胞内 NMR 在其首次推出后的 20 年间的发展和应用。回顾了用于制备细胞样品和同位素标记策略的现有方法,以及核磁共振生物反应器装置的开发,允许实时监测细胞内代谢物和蛋白质。Bax 和他的同事将他们的贡献集中在使用溶液中生物分子的弱排列和测量残余偶极耦合 (RDC) 的能力上。他们审查了为不同类型的 RDC 量身定制的独特脉冲方案,并提供了这些结构参数如何允许结构验证和改进的示例,从头结构确定,以及骨干和域运动的量化。Blackledge 及其同事通过提供描述构象能量景观的整体平均结构和动态参数,总结了 NMR 表征内在无序蛋白质 (IDP) 的独特能力。介绍了最近应用 NMR 方法来阐明功能无序组件中局部和远程动力学的性质和时间尺度。与本期大多数其他以蛋白质为中心的评论相比,Dayie 和他的同事讨论了 RNA 分子以及如何使用 NMR 来研究溶液中 RNA 的结构动力学。他们展示了选择性同位素标记如何克服大线宽、标量和偶极耦合以及光谱重叠带来的限制,特别是对于大 RNA。巧妙的标记技术与定制的脉冲序列相结合,提供了对 RNA 结构生物学重要领域的看法。Hagn 及其同事回顾了在生理相关环境中使用脂质纳米盘对膜蛋白进行 NMR 结构研究的好处。提供了当前可用和流行的脂质纳米盘系统的详细概述,包括工作流程优化。此外,还全面描述了此类脂质系统在研究膜蛋白的结构、结合、相互作用和功能动力学方面的独特优势。Hiller 及其同事说明了利用不成对电子的磁矩与核自旋之间的串扰用于结构目的的惊人潜力。由蛋白质中顺磁中心介导的大化学位移变化,称为伪接触位移 (PCS),是由这些在长距离 (≥50 Å) 上活跃的偶极-偶极相互作用产生的。描述了螯合镧系元素离子的不同标签以及它们在大型生物分子复合物和活细胞内的用途。Pierattelli 及其同事展示了一套13 C 检测的多核实验,可提供有关蛋白质的独特信息。13 C优于1的优点讨论了 H 检测,并提出了需要考虑的重要技术方面。此外,这些类型的实验完美地补充了传统质子光谱的实例也被突出显示。用于回答结构生物学问题的细胞内 NMR 新兴领域是 Theillet 及其同事审查的中心。强调了不同原子核提供的原子尺度信息的通用性和独特性。此外,还简要概述了细胞内结构生物学中的其他主要技术,如 EPR、smFRET 和 cryo-ET,以及与这些互补方法相比,细胞内 NMR 的相对优缺点。Ubbink 及其同事提供了以生物核磁共振中使用的最先进的顺磁标签为中心的全面概述。特别强调合成路线及其不同的化学性质。作者深入讨论了针对各种应用的特定标签的优缺点。独特的是,该贡献还描述了专为通过 NMR 和 EPR 光谱学进行 DNA 和 RNA 结构研究而设计的顺磁性标签。八篇评论涵盖了生物固体的固态 NMR 方法。Agarwal 及其同事向读者介绍了与最先进的生物学应用相关的静态和魔角旋转 (MAS) 固态 NMR 光谱的方法学基础,以及通过固态 NMR 解决的蛋白质结构的具体示例. Corzilius 及其同事的综合论文侧重于动态核极化 (DNP) 的新兴领域,对机制、极化剂、以及 DNP 增强核磁共振在生物学问题上的最新应用。Chow、De Paëpe 和 Hediger 全面介绍了最先进的 DNP 仪器、实验方案和样品制备方面的策略和挑战,以及在蛋白质折叠/错误折叠/紊乱、核酸中的广泛应用、病毒、膜蛋白、细胞壁和细胞和细胞外环境中的生物分子。Hong 及其同事对 细胞和细胞外环境中的核酸、病毒、膜蛋白、细胞壁和生物分子。Hong 及其同事对 细胞和细胞外环境中的核酸、病毒、膜蛋白、细胞壁和生物分子。Hong 及其同事对19 F-和1基于 H 的 MAS NMR 方法用于生物系统中的相关光谱和距离测量,涵盖蛋白质、核酸和碳水化合物,以及它们的复合物和组装体。Hou 及其同事通过 MAS NMR 回顾了偶极和化学位移重偶联方法的当前进展,展示了生物分子结构和动力学研究的优雅应用。Pintacuda 及其同事讨论了新兴的巡回演出方法和高频 MAS NMR 的应用,这导致了该领域的“灵敏度和分辨率革命”,并为具有挑战性的生物组件的结构和动力学分析打开了大门。Reif 的精彩评论描述了氘代和质子检测在生物系统的高分辨率 MAS NMR 光谱中的多种用途,包括用于共振分配的标记策略和实验方法以及结构和动力学的定量表征。Wang 和同事讨论了最先进的 MAS NMR 和 DNP 增强的 MAS NMR 技术,以研究藻类、细菌、真菌和植物的细胞外基质和细胞壁的结构组织和动态特性。他们讨论了可以从其他技术无法获得的这些无处不在的生物材料中获得的独特见解。我们热烈感谢所有按承诺及时提交评论的作者,并及时将其收录在本专题的印刷版中,并希望读者发现它们是愉快的、信息丰富的和令人振奋的。编辑部的努力 Wang 和同事讨论了最先进的 MAS NMR 和 DNP 增强的 MAS NMR 技术,以研究藻类、细菌、真菌和植物的细胞外基质和细胞壁的结构组织和动态特性。他们讨论了可以从其他技术无法获得的这些无处不在的生物材料中获得的独特见解。我们热烈感谢所有按承诺及时提交评论的作者,并及时将其收录在本专题的印刷版中,并希望读者发现它们是愉快的、信息丰富的和令人振奋的。编辑部的努力 Wang 和同事讨论了最先进的 MAS NMR 和 DNP 增强的 MAS NMR 技术,以研究藻类、细菌、真菌和植物的细胞外基质和细胞壁的结构组织和动态特性。他们讨论了可以从其他技术无法获得的这些无处不在的生物材料中获得的独特见解。我们热烈感谢所有按承诺及时提交评论的作者,并及时将其收录在本专题的印刷版中,并希望读者发现它们是愉快的、信息丰富的和令人振奋的。编辑部的努力 我们热烈感谢所有按承诺及时提交评论的作者,并及时将其收录在本专题的印刷版中,并希望读者发现它们是愉快的、信息丰富的和令人振奋的。编辑部的努力 我们热烈感谢所有按承诺及时提交评论的作者,并及时将其收录在本专题的印刷版中,并希望读者发现它们是愉快的、信息丰富的和令人振奋的。编辑部的努力化学评论非常感谢通过审查过程引导论文并将它们组装到这个问题中。Angela M. Gronenborn 是匹兹堡大学 UPMC Rosalind Franklin 教授和结构生物学系系主任,自 2005 年以来一直在该大学工作。她获得了博士学位。1978 年在德国科隆大学获得化学博士学位。她实验室的一项主要研究重点是了解生物大分子如何根据其结构和动力学工作。她的团队以综合方式将核磁共振 (NMR) 光谱学和其他结构技术与生物物理学、生物化学和化学相结合,以研究与人类疾病相关的分子和原子水平的细胞过程。由于她的研究贡献,她获得了多个奖项的认可,包括 Mildred Cohen 生物化学奖、Richard R. Ernst 磁共振奖、E. Bright Wilson 光谱学奖和生物物理学会创始人奖。她曾入选美国国家科学院、挪威科学与文学院、德国国家科学院和美国艺术与科学院。Tatyana Polenova 是特拉华大学的化学和生物化学教授。她于 1992 年获得莫斯科国立大学的本科学位(优异文凭)。她获得了博士学位。1997年获得哥伦比亚大学博士学位,在Ann McDermott教授的实验室工作。在哥伦比亚大学获得博士后职位后,她于 1999 年加入纽约城市大学亨特学院,2003 年,她搬到了特拉华大学。她的研究重点是固态核磁共振方法的开发和应用,以了解生物系统的结构、动力学和功能,包括病毒和细胞骨架蛋白组装。Polenova 是国际磁共振学会的会员。她是主编Journal of Magnetic ResonanceJournal of Structural BiologyJournal of Structural Biology: X的副主编,以及Journal of Biomolecular NMR的副主编。这篇文章尚未被其他出版物引用。
更新日期:2022-05-25
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