Study of Allosteric Proteins by NMR

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DESCRIPTION (provided by applicant): The atomic-scale delineation of allosteric mechanisms has contributed much to the understanding of biomolecular function. Dr. Zuiderweg has obtained preliminary data that will allow us to study by nuclear magnetic resonance spectroscopy in solution (NMR), the allosteric mechanisms of Hsp70 proteins. NMR is capable of integrating the study of structure, dynamics and interactions and is therefore likely to contribute to the fundamental understanding of allosterics, which thus far has been almost exclusively derived from comparisons of structures of proteins embedded in crystals. Dr. Zuiderweg has chosen the Hsp70 chaperone protein system as a target for his studies because its allosteric mechanism is currently unknown. The Hsp70's play a central role as the most abundant and most conserved systems aiding protein folding in vivo. Understanding of the functioning of these molecules is thus of relevance for the development of therapies for protein folding diseases. With newly developed NMR methods such as TROSY, spectral simplification by deuteration and specific labeling and the measurement of residual dipolar couplings, it is currently possible to study large proteins in solution at atomic resolution. As such, the study of allosteric proteins by NMR has come within reach; his target is 55 kDa. This first structural study of an allosterically functional Hsp70 protein will help delineate the conformational/dynamical changes that govern the allosteric coupling between nucleotide and substrate-binding domains. By NMR, it is possible to study these changes in solution, and monitor the effects on these parameters of adding different nucleotides, substrates, and co-factors such as phosphate, magnesium and potassium. In order to do so, Dr. Zuiderweg will first concentrate on the NMR description of the properties of 44 kDa nucleotide binding domains. In the next stage, Dr. Zuiderweg will move onward to the 55 kDa construct, and study its molecular parameters as a function of nucleotide and substrate binding combined. In order to facilitate this task, Dr. Zuiderweg will aim for the study of such a construct of the Dnak chaperone of the thermophilic bacterium Thermus thermophilus, which can be studied at elevated temperatures and hence gives rise to excellent NMR spectra.