Integrating 19F distance restraints for accurate protein structure determination and characterization of HIV-1 protein assemblies by magic angle spinning NMR spectroscopy
Date
2024
Authors
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Publisher
University of Delaware
Abstract
Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy is used for atomic-level characterization of structure and dynamics of molecules and assemblies. For protein structure determination by MAS NMR spectroscopy, 13C, 15N, and 1H-detected multidimensional experiments are typically employed to extract interatomic distance information and site-specific details. However, the inherently local nature of the information extracted from these experiments, with an upper limit of 6-8 Å, often limits the accuracy of the resulting structures. To obtain longer-range distance information, one can implement different isotopic labeling schemes utilizing alternative nuclei to characterize complex biological systems, including multi-domain proteins and macromolecular assemblies. In Chapter 1, I give an overview of MAS NMR spectroscopy as a technique for the characterization and structure determination of proteins. I discuss strategies for incorporating fluorine nuclei as powerful NMR probes for studying the structure and function of biological systems. ☐ In Chapter 2, I present a novel application of 19F fast MAS NMR spectroscopy for protein structure determination. In our earlier studies, we exploited the favorable spectroscopic properties of fluorine to develop 19F fast MAS NMR spectroscopy as a tool for structural studies of proteins and protein assemblies. Herein, we explore the integration of 19F-based distance restraints in protein structure determination by MAS NMR spectroscopy. Using 4F-Trp,U-13C,15N crystalline Oscillatoria agardhii agglutinin (OAA) as a model system, we demonstrate that judiciously designed 2D and 3D 19F-based dipolar correlation experiments such as (H)CF, (H)CHF, and FF, can yield interatomic distances in the 8-16 Å range. Incorporation of fluorine-based restraints into structure calculation permitted to more precisely define regions in the protein around the fluorine-containing residues with notable improvements observed for residues in proximity to the carbohydrate-binding loops Trp pairs (W10/W17 and W77/W84) which lacked sufficient long-range 13C-13C distances. Our work highlights the use of fluorine and 19F fast MAS NMR spectroscopy as a powerful structural biology tool. ☐ In chapter 3, I discuss my contributions to other projects and papers I co-authored over the course of my Ph.D. studies.
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Keywords
Magic-angle spinning, Nuclear magnetic resonance spectroscopy, Atomic-level characterization, Biological systems, Oscillatoria agardhii