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Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy (PhD)

Degree Program

Biochemistry

Year Degree Awarded

2019

Month Degree Awarded

February

First Advisor

Prof. Lynmarie Thompson

Subject Categories

Biochemistry, Biophysics, and Structural Biology

Abstract

Bacteria employ remarkable membrane-bound nanoarrays to sense their environment and direct their swimming. Arrays consist of chemotaxis receptor trimers of dimers that are bridged at their membrane-distal tips by rings of two cytoplasmic proteins, a kinase CheA and a coupling protein CheW. It is widely accepted that ligand binding to the receptor causes a 2 Å piston motion of a helix that extends through the periplasmic and transmembrane domains. However, it is not clear how the signal propagates 200 Å further to control activity of the kinase bound at the tip of the receptor. Dynamic changes within the cytoplasmic domain of the receptor have been proposed to play a key role in signal transmission. To test these proposals, we applied solid-state NMR to study the structure and dynamics of the E coli Asp receptor cytoplasmic fragment (U-13C,15N-CF) in native-like arrays of functional complexes with CheA and CheW. To detect segments that experience motions on the millisecond time scale, we use a 15N{13C} REDOR filter to remove signals from rigid backbone carbons and retain signals from backbone carbons with ms-timescale dynamics. This experiment exhibits only 60-70% of the expected REDOR dephasing, suggesting that 40-30% of the backbone has ms-timescale mobility that averages the ~ 1000 Hz 13C15N dipolar couplings. A novel REDOR-filtered DARR experiment led us to identify MH2 (methylation helix 2) as the region with ms-timescale motion. INEPT spectra reveal dynamics on the ns or shorter timescale. The INEPT-detectable regions are identified through a combination of biochemical and NMR approaches, to establish that MH1 (methylation helix 1) is mobile on the ns timescale. Interestingly, the INEPT and REDOR studies indicate the methylation region has asymmetric mobility: MH1 has ns-timescale dynamics that increase in the kinase-off state, and MH2 has ms-timescale dynamics that decrease in the kinase-off state. Thus these NMR measurements of the dynamics of CF within its functional complexes provide insight into the structural organization and signaling-related changes of the receptor methylation region, which is responsible both for transmitting the ligand-binding signal and for adaptation, both of which are critical to the chemotaxis response.

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