Type of Document	Dissertation
Author	Achuthan, Srisairam
Author's Email Address	sairam.achuthan@gmail.com
URN	etd-11132006-141131
Title	Analysis of Orientational Restraints in Solid-State Nuclear Magnetic Resonance with Applications to Protein Structure Determination
Degree	Doctor of Philosophy
Department	Mathematics, Department of
Advisory Committee	Advisor Name Title John R. Quine Committee Chair DeWitt Sumners Committee Member Richard Bertram Committee Member Timothy A. Cross Committee Member
Keywords	Intensity Analysis Frenet Frames Orientational Restraints Protein Structures
Date of Defense	2006-10-04
Availability	unrestricted
Abstract Of late, path-breaking advances are taking place and flourishing in the field of solid-state Nuclear Magnetic Resonance (ssNMR)spectroscopy. One of the major applications of ssNMR techniques is to high resolution three-dimensional structures of biological molecules like the membrane proteins. An explicit example of this is PISEMA (Polarization Inversion Spin Exchange at Magic Angle). This dissertation studies and analyzes the use of the orientational restraints in general, and particularly the restraints measured through PISEMA. Here, we have applied our understanding of orientational restraints to briefly investigate the structure of Amantadine bound M2-TMD, a membrane protein in Influenza A Virus. We model the protein backbone structure as a discrete curve in space with atoms represented by vertices and covalent bonds connecting them as the edges. The oriented structure of this curve with respect to an external vector is emphasized. The map from the surface of the unit sphere to the PISEMA frequency plane is examined in detail. The image is a powder pattern in the frequency plane. A discussion of the resulting image is provided. Solutions to PISEMA equations lead to multiple orientations for the magnetic field vector for a given point in the frequency plane. These are duly captured by sign degeneracies for the vector coordinates. The intensity of NMR powder patterns is formulated in terms of a probability density function for 1-d spectra and a joint probability density function for the 2-d spectra. The intensity analysis for 2-d spectra is found to be rather helpful in addressing the robustness of the PISEMA data. To build protein structures by gluing together diplanes, certain necessary conditions have to be met. We formulate these as continuity conditions to be realized for diplanes. The number of oriented protein structures has been enumerated in the degeneracy framework for diplanes. Torsion angles are expressed via sign degeneracies. For aligned protein samples, the PISA wheel approach to modeling the protein structure is adopted. Finally, an atomic model of the monomer structure of M2-TMD with Amantadine has been elucidated based on PISEMA orientational restraints. This is a joint work with Jun Hu and Tom Asbury. The PISEMA data was collected by Jun Hu and the molecular modeling was performed by Tom Asbury.
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