Computations of structures of protein assemblies from experimental magic angle spinning NMR restraints
Date
2023
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Publisher
University of Delaware
Abstract
This dissertation concerns with computational aspects of protein structure determination from experimental magic angle spinning nuclear magnetic resonance (MAS NMR) data and by integrating MAS NMR experimental restraints with information obtained by other structural biology techniques, such as cryogenic electron microscopy (cryo-EM) and X-ray crystallography. ☐ In Chapter 1, protein structure calculation approaches are introduced. ☐ Although the framework for NMR protein structure determination has existed for quite some time, the general requirements for obtaining accurate and precise structures, particularly in the solid state, have not been established until recently. Therefore, we have performed a systematic model study to quantify accuracy and precision with varying numbers of distance restraints. The results of this work are discussed in Chapter 2. ☐ Chapter 3 focuses on structure calculations of two crystalline systems: (1) the N-terminal domain (NTD) of SARS-CoV-2 nucleocapsid protein, and (2) the crystalline array of HIV-1 CACTD-SP1 protein bound with assembly co-factor IP6 and a maturation inhibitor Bevirimat (BVM). ☐ Chapters 4 and 5 concern with an integrated approach to determine atomic-resolution structures of large biological assemblies, whereas MAS NMR restraints are combined with information from other experimental and computational methods. In Chapter 4, the structure of tubular assemblies of HIV-1 CA capsid protein is presented, determined by integrating MAS NMR restraints with cryo-EM density in data-driven molecular dynamics (MD) simulations. In Chapter 5, this general approach is expanded and adapted to determine the structure of a motor domain of conventional kinesin-1, KIF5B, bound to polymerized microtubules. The studies presented in these two chapters establish the integrative structural biology framework for determination of structures of large biological systems inaccessible by any single technique in isolation.
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Keywords
NMR restraints, Protein assemblies, Magic angle spinning