UC Berkeley

Molecular motors transduce chemical energy –usually from ATP hydrolysis– into directed motion and mechanical work, which is used to perform key functions in almost every cellular process. Molecular motors are particularly important in the maintenance of cellular proteostasis, i.e. the equilibrium between protein synthesis and degradation. ATP-dependent proteases of the AAA+ family, such as ClpXP from Escherichia coli and the eukaryotic 26S proteasome, play a central role in protein degradation. Given its extensive biochemical and structural characterization, ClpXP is a paradigm for the study of the operating principles of eukaryotic and prokaryotic protease machines of the AAA+ family. However, the molecular mechanism by which ClpXP couples the energy from ATP hydrolysis into mechanical work is still poorly understood. Here we used biochemical and single-molecule assays with optical tweezers to directly probe the operation of ClpXP as it unfolds and translocates its protein substrate.

Chapter one provides an introduction into the structure and function of ClpXP, which is considered an archetype for the study of AAA+ proteases. This chapter also introduces key concepts about single molecule studies assays with optical tweezers.

Chapter two focuses on the study of the mechanisms of force generation and intersubunit coordination of ClpXP. We establish that ClpXP translocates its substrate by using cycles of alternating dwell/burst phases. Phosphate release is the force generating step in the ATP cycle, and ClpXP translocates its substrate in bursts resulting from highly coordinated conformational changes in two to four ATPase subunits. Based on our results, we propose a model where ClpXP must use its maximum firing capacity of four subunits to unfold stable substrates like GFP. Interestingly, the average dwell duration between individual bursts of translocation is constant, regardless of the number of translocating subunits, implying a constant translocation cycle governed by an unidentified “internal clock”. Together, our results indicate that ClpXP operates with constant “rpm” but uses different “gears”.

Chapter three describes the complete mechanochemical cycle of ClpXP, as well as the coupling and power efficiency of the motor. We show that ADP release and ATP binding happen non-sequentially during the dwell, while ATP hydrolysis and phosphate release occur during the burst. ADP release is the rate-limiting transition of the ATP cycle. Interestingly, the size of the highly-conserved translocating loops within the ClpX pore has been evolutionarily optimized to maximize motor power generation, as well as the coupling between chemical and mechanical cycles of the motor. Finally, we presente evidence showing that the conformational resetting of these loops between consecutive bursts seems to determine ADP release from individual ATPase subunits and the overall duration of the motor’s cycle, which explains the observed “internal-clock mechanism” of ClpXP.