Nuclear Magnetic Resonance (NMR) has immense potential in providing atomic-level information on the mechanism of action of diverse biological systems such as globular proteins, membrane proteins, lipids, nucleic acids, biofibrils and biomaterials. While some applications of the high-resolution NMR spectroscopic technique correlate the structure with function, others are concerned with the dynamics of biomolecules interacting with other bio- or non-biomolecular systems such as nanomaterials. Recent advances in this field have led to the advent of novel approaches and techniques which go beyond the conventional NMR experiments used in structural biology. Thus, the integration of diverse techniques is necessary to bridge the gap between structural and functional studies so as to provide a comprehensive understanding of dynamic NMR. The initial planning of this book was carried out with Prof. Anirban Bhunia and Prof. H. S. Atreya. However, the untimely demise of Prof. Atreya in 2020, while we were in the middle of this compilation process has been an inexpressible loss to us. We reorganized and started with Prof. Neeraj Sinha, who incorporated several important applications of solid-state NMR in the book.
The book has been compiled in such a way that the initial section deals with the basics of dynamics and relaxations of NMR spectroscopy. The next section deals with various applications in the solution state NMR methodologies including protein–ligand interactions, saturation transfer difference (STD) NMR, dynamics of protein–nanoparticle interactions, and large protein complexes. The final part of the book contains applications of solid-state NMR concerned with protein–mineral interfaces, G Protein Coupled Receptor (GPCRs), protein fibrils, and biomaterials such as bone, cartilage, etc. Chapter 1 discusses the basics of triple-resonance experiments for assignments and structure elucidation of biomolecules. Additionally, the authors also discuss the characterization of sparsely populated protein conformations using recent NMR methodologies. In Chapter 2, Harindranath Kadavath and Roland Riek discuss the principles of exact nuclear Overhauser enhancement (eNOE) and its recent application in multistate structural ensembles. L. Jaremko and co-workers (Chapter 3) have provided various NMR spin relaxation mechanisms and NMR methodologies used to probe these relaxation rates. This chapter nicely illustrates the investigation of molecular motions over practically all timescale ranges.
In Chapter 4, Linda Nicholson and co-workers present the recent advances of NMR lineshape analysis in probing protein dynamics; and determining the kinetics and thermodynamics of multistate reaction schemes with examples. Ipsita Chakraborty and Rangeet Bhattacharyya (Chapter 5) present an interesting case study that uses a simple, real-time NMR method of measuring the relaxation of solvent to quantitatively monitor the dynamics of the aggregation of smart polymers. Cristinal Airoldi and co-workers (Chapter 6) present an overview of the current status of the applications of NMR spectroscopy to monitor ligand–receptor interactions using STD NMR, WaterLOGSY, trNOESY, DOSY-based, and relaxation filters. In addition, they have commented on the weaknesses of these methods and described on-cell NMR methods in molecular recognition using HR-MAS. Chapter 7 by Angulo and Monaco explains several important STD NMR techniques that monitor interactions and presents the latest developments in this field.
Bhunia and co-workers in Chapter 8 focus on Dark State Exchange Saturation Transfer (DEST) NMR as a tool to map slow chemical exchange at functional protein interfaces. Adeptly, the DEST experiment is introduced as an extension to the original STD technique and the details of the NMR pulse sequence and quantitative data analysis using Bloch–McConnell equations are explained. Finally, its application to several IDPs is discussed. Chapter 9 summarizes the information on different chemical biology tools and techniques used for characterizing molecular interactions among nanoparticles and proteins. Surajit Bhattacharjya in Chapter 10 describes NMR structural and dynamical studies of leucocyte-specific β2 integrin cytosolic tails with cognate proteins. The transient nature of the tail–tail and tail–protein interactions are refractory to other methods for determining its atomic-resolution structure. The NMR based 3-D structures of α and β cytosolic tails and tail/tail complexes; in addition, the complexes of β2 tail with integrin activator and repressor proteins are discussed in this chapter. Chapter 11, by Hiller and Burmann, explains the dynamics of big complexes such as chaperones and their client proteins. The authors elegantly describe the various NMR approaches including CSPs, NOEs, hydrogen–deuterium exchange, relaxation, PRE, and also other biophysical experiments to study the lifetimes of the complexes and understand the kinetics of the interactions.
Rui Huang in Chapter 12 discusses how NMR spectroscopy, specifically 13C-methyl-TROSY, can be used to probe co-operativity in large proteins and protein–protein complexes. This chapter includes the general principle of the methyl-TROSY technique, the challenges in the sample preparation of the NMR-active methyl group labels on the specific amino acids, along with different biosynthetic labelling approaches, e.g., E. coli vs. cell free. Chapter 13 by Gooley and co-workers dwells on the various applications of NMR methods to study GPCR structure, dynamics, and ligand interactions. The authors provide an overview of GPCR structure, followed by the structural rearrangements associated with receptor activation. Subsequently, various expression systems in vogue, labelling strategies, as well as membrane-mimicking systems used for encapsulating GPCRs to express and purify receptors in manners suitable for NMR studies are described. Prototypical adrenergic and adenosine receptors, and more recent opioid receptors are discussed also. Chapter 14, by Hansen and co-workers, comprehensively surveys the study of intrinsically disordered proteins (IDPs) using CPMG-based NMR techniques in conjunction with molecular dynamics (MD) simulation. Koh in Chapter 15 discusses the recent developments in NMR strategies for higher-ordered structure analysis of biopharmaceuticals, improvement of protein druggability, and understanding of the cell permeabilization activity of medium-size molecules.
The methodology of solid-state NMR spectroscopy is increasing rapidly in terms of ultra-high-speed magic angle spinning. This has opened up new frontier in terms of applications. The final section of the book covers these important developments. In Chapter 16, Nishiyama describes methods to locate hydrogen atoms in solids using fast MAS solid-state NMR and their application for atomic-resolution structural studies. One of the advantages that solid-state NMR spectroscopy provides is that we can structurally study biological systems in their native environment. Chapter 17, by F. M. Marrassi and co-authors, describes various methods to mimic native protein environments. These systems include membrane proteins and biominerals such as bone and cartilage. Chapter 18, by S. J. Opella and co-authors, describes solid-state NMR methods for membrane proteins in their native environments. The system chosen is membrane receptor CXCR1 and its interactions with agonist IL8. Chapter 19, by Markus Weingrath and co-authors, describes the application of probe antibiotics in membranes. The remainder of the chapters deal with diverse applications of solid-state NMR to the systems such as antimicrobial peptides (in Chapter 20), different native biomaterials such as bone, cartilage, teeth (in Chapter 21), and the lipid phase of stratum corneum (in Chapter 22). Overall, we have tried to cover recent methodology developments as well as diverse interface biological applications.
Firstly, we would like to thank the Royal Society of Chemistry for giving us the opportunity to edit this book. Special thanks are due to Liv Towers and Janet Freshwater for their timely support and understanding. Thanks are also expressed to all the authors and reviewers for their excellent contributions and making this compilation a success. We thank Dr Janarthanan Krishnamoorthy and Miss Dipita Bhattacharyya for their tireless support at various stages of editing this book. Finally, we extend our thanks to many other people, who contributed to this book in bringing it to its current form, despite this being our first experience in editing a book.
Bose Institute, Kolkata, India
Centre of Bio-Medical Research, Lucknow, India