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Title: Structure refinement and dynamics of proteins using residual dipolar couplings and NMR relaxation data
Author: Ball, Graeme
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2005
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NMR spectroscopy can be used to investigate the structure and dynamics of proteins, both of which can provide important insights into their functions. The aims of this project were to use residual dipolar coupling (RDC) restraints to refine the existing NMR structures of several proteins and to use relaxation data to investigate their dynamics. Three proteins were studied: two module-pair fragments from human complement regulatory proteins (DAF ~ 2,3 and C4BP~1,2) and a fatty acid binding protein from the nematode parasite Ascaris suum (ABA-1A), each of which consists of two structural elements, with a poorly defined relative orientation. Implementing experiments required for the measurement of coupling constraints led to the development of new methods for the determination of the one-bond 1DCαHαRDC. Extensive sets of RDCs were measured for C4BP~1,2 and ABA-1A using 15N and 13C labelled samples and the structure refinement protocol incorporating RDCs as restraints was optimised. Significant improvements in the quality of the refined structures were achieved. The backbone dynamics of DAF~2,3 and C4BP~1,2 were probed using relaxation data measured at two fields and the time scale and extent of back-bone motions were quantified. Finally, some evidence of small amplitude intermodular motions in the module-pair proteins DAF~2,3 and C4BP~1,2 was observed. The functional significance of these findings is discussed.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available