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The Effect of Membrane Dynamics on High-Resolution NMR of Oriented or MAS Transmembrane Polypeptides

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Citation

Farès, C. (2003). The Effect of Membrane Dynamics on High-Resolution NMR of Oriented or MAS Transmembrane Polypeptides. PhD Thesis, University of Guelph, Guelph, Ontario, Kanada.


Cite as: http://hdl.handle.net/21.11116/0000-0006-EB6D-8
Abstract
The present work provides new perspectives on the growing field of solid-state nuclear magnetic resonance (NMR) for the structural elucidation of membrane polypeptides and proteins. The effects of dynamics occuring on time scales spanning several orders of magnitude, and with widely differing geometries are emphasized. The various sections of this thesis describe the influence of motions on both well-established and novel heteronuclear multidimensional NMR experiments using both theoretical calculations and experimental measurements. Through a series of simulations, natural irregularities and motional averaging in membrane proteins were shown to strongly affect the appearance of separated local field experiments (e.g. PISEMA) and to impose limitations on structure-based assignment strategies and on the interpretation of orientation constraints. To demonstrate the influence of motions with medium-to-slow correlation times (ms to ns), a systematic study of the spin-lattice relaxation in the rotating frame was conducted for several nuclei (1H, 13C and 15N) in small membrane polypeptides, either in oriented or magic angle spinning (MAS) samples. This study not only assessed the validity of some motional models, but also characterized the magnetization relaxation rates crucial for the design of coherence transfer experiments. It was found that relaxation time constant (T) values on the order of 10-3 - 10-2 s for backbone nuclei and their dependence on sample orientation are consistent with the model of transmembrane polypeptides undergoing axial-diffusion (τc ~ 10-8 - 10-7 s) and small amplitude off-axis reorientation (τc ~ 10-6 - 10-5 s). Important considerations are explored regarding the innovative use of 1H MAS NMR to determine the structure of small membrane polypeptides undergoing significant axial diffusion. A novel correlation experiment (2D-CROPSY) is proposed based on cross-polarization between 1H and 15N. This experiment was able to resolve a majority of backbone amide 1H resonances in gramicidin A. This method was then extended to reveal structural information through 1H-1H cross-relaxation exchange, or NOES, in a combined experiment (2D-NOE-CROPSY). The significance of the NOE cross-peaks in transmembrane polypeptides was scrutinized through experimental measurements and simulations. Because of the anisotropic nature of motions in membranes, it was demonstrated that 1H- 1H cross-relaxation is highly efficient and adopts both distance and orientation dependence. Finally, an unusual case of broadening of the amide 1H resonances in 1H MAS NMR was observed in membrane polypeptides. The scale of this effect suggests that the major mechanism of this broadening effect stems from the residual electric quadrupolar coupling of the covalently-bonded and dipolar-coupled 14N.