Solid state nuclear magnetic resonance methodology and applications to structure determination of peptides, proteins and amyloid fibrils

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2003.Vita.Includes bibliographical references.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Several methodological developments and applications of multidimensional solid-state nuclear magnetic resonance to biomolecular structure determination are presented. Studies are performed in uniformly 3C, 15N isotope labeled samples with magic-angle spinning for optimal resolution and sensitivity. Frequency selective rotational-echo double-resonance (FSR) and three-dimensional transferred-echo double-resonance (3D TEDOR) methods for carbon-nitrogen distance measurements in (U-'3C,S5N)-labeled peptides and proteins are described. FSR employs frequency selective Gaussian pulses in combination with broadband REDOR recoupling to measure dipolar couplings based on the isotropic chemical shifts of the selected 13C-15N spin pairs. The experiment is demonstrated in model peptides, N-acetyl-L-Val-L-Leu and N-formyl-L-Met-L-Leu-L-Phe, where multiple distances in the 3-6 A range are determined with high precision, and in a membrane protein, bacteriorhodopsin, where the distances between aspartic acids Asp-85 and Asp-212 and the retinal Schiff base nitrogen are measured in the active site. The 3D TEDOR methods employ 13C and 15N chemical shift dimensions for site-specific resolution and encode the distance information in the buildup of cross-peak intensities, allowing multiple distances to be measured simultaneously. The methods are demonstrated in N-acetyl-L-Val-L-Leu and N-formyl-L-Met-L-Leu-L-Phe, where 20 and 26 distances up to 6 A are determined, respectively. The molecular conformation of peptide fragment 105-115 of transthyretin in an amyloid fibril is investigated.(cont.) Complete sequence-specific 13C and 15N backbone and side- chain resonance assignments are obtained using two-dimensional 13C-13C and 15N-13C-3C chemical shift correlation experiments. Backbone torsion angles are measured directly using three-dimensional dipolar-chemical shift correlation experiments, which report on the relative orientations of 3C-15N, 3C-1H and 15N-'H dipolar tensors, and intramolecular 13C-15N distances in the 3-5 A range are determined using 3D TEDOR, resulting in about 60 constraints on the peptide structure. An atomic-resolution structure of the peptide consistent with the NMR constraints is calculated using simulated annealing molecular dynamics, and the results indicate that the peptide adopts an extended β-strand conformation in the fibril.by Christopher Peter Jaroniec.Ph.D