Date of Award
Doctor of Philosophy (PhD)
Lynmarie K. Thompson
Robert M. Weis
Craig T. Martin
Calixarene, Chemotaxis, Fluorotoluene, REDOR, TCUP, Trimer-of-dimers
The receptor dimers that mediate bacterial chemotaxis form high-order signaling complexes with CheW and the kinase CheA. From the packing arrangement in two crystal structures of different receptor cytoplasmic fragments, two different models have been proposed for receptor signaling arrays: the trimers-of-dimers and hedgerow models. We identified an interdimer distance that differs substantially in the two models, labeled the atoms defining this distance through isotopic enrichment, and measured it with 13C-19F REDOR. This was done in two types of receptor samples: first, isolated bacterial membranes containing overexpressed, intact receptor, and second, soluble receptor fragments reconstituted into kinase-active signaling complexes. In both cases, the distance found was not compatible with the receptor dimer−dimer contacts observed in the trimers-of-dimers or in the hedgerow models. Comparisons of simulated and observed REDOR dephasing were used to deduce a closest-approach distance at this interface, which provides a constraint for the possible arrangements of kinase-competent receptor assemblies. An alternate model of receptor signaling is proposed, which reconciles this result with existing structural and biochemical data. Additionally, two advances to solid-state NMR methodology are described. The first is a set of strategies to protect protein samples against degradation by solid-state NMR analysis. Biochemical and spectroscopic techniques are prescribed to identify and isolate specific challenges to protein stability, allowing them to be addressed individually. For this purpose a new pulse sequence (Thermal Calibration Under Pulseload, or TCUP) is employed, which allows sample temperature to be measured with exceptional time resolution. The second NMR advance describes the creation and characterization of a 13C-19F REDOR distance-calibration standard. The inclusion compound of 4-fluorotoluene and tert-butylcalixarene was used for this purpose. The compound is easily synthesized from commercially available materials, and provides a long, isolated 13C-19F distance of 4.1 Å. Dynamics within the compound allow direct observation of 19F resonances without 1H-decoupling, and provide exceptionally sharp 13C resonances; these characteristics speed the routine setup of REDOR experiments. Both methodological developments were important to performing accurate distance measurements on functionally relevant chemotaxis signaling complexes; they also pave the way for making similar measurements in other proteins of interest.
Fowler, Daniel John, "Quaternary Structure of Chemoreceptors in Active Signaling Complexes Differs From Crystal Structure of Isolated Fragments: Evidence From Solid-State NMR" (2010). Open Access Dissertations. Paper 205.