Date of Award
Doctor of Philosophy
Solid-state NMR spectroscopy is an important tool for studying the chemical and three-dimensional structures of organic and inorganic solids because of its intrinsic atomic-level structural information, nonperturbing nature, and the large range of dynamic time scales. It is especially powerful in studying insoluble and noncrystalline membrane proteins, which are difficult to analyze by traditional X-ray crystallography or solution NMR techniques. In this thesis, various NMR techniques are used to study the structure and dynamics of membrane proteins within lipid bilayers.
The main protein we are focusing on is human neutrophil peptide 1 (HNP-1). It is a small cysteine-rich cationic antimicrobial protein found in human neutrophils. It forms the first line of defense by the innate immune system of humans against pathogens. The antimicrobial activity of HNP-1 is believed to be caused by disruption of the microbial cell membrane and various models of HNP-membrane interaction have been proposed. However, none of these mechanistic models are based on structure information from the lipid bilayer. Therefore, understanding the peptide structure in the presence of membrane and its interaction with the lipids will shed light on the antimicrobial mechanism of HNP-1. As a first step, we have calculated the minimum-energy structures of uniformly 13C, 15N-labeled microcrystalline HNP-1 based on all NMR torsion angle and distance restraints determined by various 2D and 3D correlation techniques. The solid-state NMR structure has close similarity to the crystal structures of the HNP family. Then we reconstituted HNP-1 into DMPC/DMPG lipid bilayers. We confirmed that the protein is predominantly dimerized at high protein/lipid molar ratios by 19F spin diffusion experiments. Various methods under magic-angle spinning (MAS) such as 13C-31P REDOR, 1H spin diffusion and 13C DIPSHIFT have been utilized to study the interaction of HNP-1 with lipid bilayers. The experimental results strongly support a "dimer pore" topology of HNP-1 in which the polar top of the dimer lines an aqueous pore while the hydrophobic bottom faces the lipid chains.
The second focus of this thesis is the oriented bicelle alignment , we have studied the alignment of bicelles with different lipids combinations, long- to short-chain lipid ratios, hydration levels and a phase diagram was generated. We also show that the orientation of a protein called HNP-1, which has 3 β-strands and dimerizes, can be simulated by predicting the correlation of the 15N anisotropic chemical shift and the N-H dipolar coupling.
Zhang, Yuan, "Investigation of Antimicrobial Peptides in Lipid Membranes by Solid-State NMR" (2011). Graduate Theses and Dissertations. 10291.