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The Structural Dynamic Properties of Proteins Illuminated by Solution NMR

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The Structural Dynamic Properties of Proteins Illuminated by Solution NMR International Journal of Molecular Sciences Review Spotlight on the Ballet of Proteins: The Structural Dynamic Properties of Proteins Illuminated by Solution NMR Yuji Tokunaga 1 , Thibault Viennet 2,3 , Haribabu Arthanari 2,3,* and Koh Takeuchi 1,* 1 Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan; [email protected] 2 Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; [email protected] 3 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA * Correspondence: [email protected] (H.A.); [email protected] (K.T.) Received: 22 February 2020; Accepted: 4 March 2020; Published: 6 March 2020 Abstract: Solution NMR spectroscopy is a unique and powerful technique that has the ability to directly connect the structural dynamics of proteins in physiological conditions to their activity and function. Here, we summarize recent studies in which solution NMR contributed to the discovery of relationships between key dynamic properties of proteins and functional mechanisms in important biological systems. The capacity of NMR to quantify the dynamics of proteins over a range of time scales and to detect lowly populated protein conformations plays a critical role in its power to unveil functional protein dynamics. This analysis of dynamics is not only important for the understanding of biological function, but also in the design of specific ligands for pharmacologically important proteins. Thus, the dynamic view of structure provided by NMR is of importance in both basic and applied biology. Keywords: solution NMR; protein function; dynamics; interaction; conformational entropy; drug development 1. Introduction Solution nuclear magnetic resonance (NMR) spectroscopy plays a critical role in providing quantitative information at atomic resolution on the functional dynamics of biomolecules in physiological conditions. NMR can not only be used to determine high-resolution structures of macromolecules, but also to analyze dynamic systems, including the characterization of protein conformational equilibria, conformational changes upon the binding to ligands, tautomeric states, transiently formed interactions, intrinsically disordered regions, and liquid–liquid phase separations. The capacity of NMR to analyze protein and DNA dynamics was described from the very beginning of its application to macromolecules when NMR revealed and characterized the aromatic ring flips in bovine pancreatic trypsin inhibitor (BPTI) [1], permitted by the conformational breathing of the protein. However, since then the development and application of solution NMR techniques have unveiled the functional dynamics of a number of important biological systems, including G protein-coupled receptors (GPCRs), ion channels, and enzymes such as kinases and small GTPases (Figure1). Int. J. Mol. Sci. 2020, 21, 1829; doi:10.3390/ijms21051829 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW 2 of 16 populated protein conformations (>0.5%) that are not readily accessible to other structural methods. For this purpose, relaxation dispersion measurements give quantitative information about a relatively slow (μsec to msec) timescale equilibrium. In the Carr–Purcell–Meiboom–Gill (CPMG)- type relaxation dispersion experiment, inversion pulses are applied at an array of frequencies during the fixed transverse relaxation period. A residue that does not undergo conformational exchange will experience one chemical shift and the corresponding intensity will not depend on the CPMG frequency. However, the chemical shift of a residue that experiences conformational exchange will oscillate between the various conformers and hence the intensity of the corresponding resonance will depend on the CMPG frequency. The effective transverse relaxation rate measured as a function of pulsing frequency harbors information about the exchange rate, the population of the states, and the chemical shift difference between the states. Furthermore, quantitative psec to nsec dynamics measurements by NMR allow the estimation of conformational entropy, which essentially reflects the number of the accessible conformations in a macromolecule. Conformational entropy mostly represents the amplitude of the fluctuation of bond vectors in a macromolecule, which can be quantified as squared order parameters by NMR relaxation analyses. NMR-based relaxation experiments can be used to derive order parameters. Thus, NMR plays a crucial role in revealing the essential contribution of the fast-conformational fluctuation of protein in regulating protein–protein affinities and allosteric regulations. Here, we will summarize recent applications of NMR to the dynamicsInt. J. Mol. Sci. of2020 biologically, 21, 1829 important systems and how this technique contributes to our understanding2 of 17 of their functional mechanisms and dynamics-guided, structure-based drug developments. Figure 1. Timescale of functional dyna dynamicsmics and the apparent molecular weights of systems where dynamics were measured using NMR. Time scale ofof NMR-identifiedNMR-identified functional dynamics depicted versus thethe apparent apparent molecular molecular weight weight of the of measured the measured system (inclusivesystem (inclusive of the micelle of orthe reconstituted micelle or reconstitutedhigh-density lipoproteinhigh-density (i.e., lipoprotein nanodiscs) (i.e., in nanodisc the cases) ofin membranethe case of membrane proteins) are proteins) shown. are It shown. should Itbe should noted be that noted the that figure the highlights figure highlights only the only timescales the timescales that have that have been been shown shown to be to essential be essential for forfunctional functional dynamics dynamics in NMR;in NMR; however, however, timescales timescale beyonds beyond those those depicted depicted in thein the figure figure may may also also be befunctionally functionally relevant. relevant. GCPR: GCPR: G-protein-coupled G-protein-coup receptors;led receptors; VDAC: VDAC: voltage-dependent voltage-dependent anion channel; anion channel;CAP: catabolite CAP: activatorcatabolite protein; activator Gα :protein; G-protein Gα alpha: G-protein subunit; alpha KcsA: subunit K channel; KcsA: of streptomyces K channel A;of streptomycesMAPK: mitogen-activated A; MAPK: mitogen-activated protein kinase; DHFR: protein dihydrofolate kinase; DHFR: reductase. dihydrofolate reductase. In combination with stable isotope labeling, NMR can analyze protein dynamics with atomic resolution without the introduction of any chemical modifications to the protein that could potentially change its dynamic properties. In addition, NMR can uniquely provide access to the lowly populated protein conformations (>0.5%) that are not readily accessible to other structural methods. For this purpose, relaxation dispersion measurements give quantitative information about a relatively slow (µsec to msec) timescale equilibrium. In the Carr–Purcell–Meiboom–Gill (CPMG)-type relaxation dispersion experiment, inversion pulses are applied at an array of frequencies during the fixed transverse relaxation period. A residue that does not undergo conformational exchange will experience one chemical shift and the corresponding intensity will not depend on the CPMG frequency. However, the chemical shift of a residue that experiences conformational exchange will oscillate between the various conformers and hence the intensity of the corresponding resonance will depend on the CMPG frequency. The effective transverse relaxation rate measured as a function of pulsing frequency harbors information about the exchange rate, the population of the states, and the chemical shift difference between the states. Furthermore, quantitative psec to nsec dynamics measurements by NMR allow the estimation of conformational entropy, which essentially reflects the number of the accessible conformations in a macromolecule. Conformational entropy mostly represents the amplitude of the fluctuation of bond vectors in a macromolecule, which can be quantified as squared order parameters by NMR relaxation analyses. NMR-based relaxation experiments can be used to derive order parameters. Int. J. Mol. Sci. 2020, 21, 1829 3 of 17 Thus, NMR plays a crucial role in revealing the essential contribution of the fast-conformational fluctuation of protein in regulating protein–protein affinities and allosteric regulations. Here, we will summarize recent applications of NMR to the dynamics of biologically important systems and how this technique contributes to our understanding of their functional mechanisms and dynamics-guided, structure-based drug developments. 2. NMR Unveils Protein Dynamics that Dictate Functions in Key Biological Systems. 2.1. G-Protein-Coupled Receptors (GPCRs) GPCRs are membrane proteins that make up a major class of cellular receptors for external stimuli. GPCRs dictate a plethora of diverse cellular physiological responses, and are therefore an important therapeutic target. Recent breakthroughs in the structure determination of GPCRs and GPCR–transducer complexes by X-ray crystallography have made significant contributions to the understanding of the molecular mechanism of GPCR activation [2]. However, a complete understanding of GPCR activation by various agonists as well as the structural changes that occur upon antagonist binding cannot be elucidated without dynamics information.
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