Elastic analysis of structural ensemble reveals the energetic basis of hand-over-hand in a AAA+ motor

Abstract

Proteins carry out cellular functions by changing their structure among a few conformations, each characterised by a different energy level. Therefore, structural changes, energy transformations, and protein function are intimately related. Despite its central importance, this relationship remains elusive. For example, while many hexameric ATPase motors are known to function using a hand-over-hand alternation of subunits, how energy transduction throughout the assembly structure drives the hand-over-hand mechanism is not known. In this work, we unravel the energetic basis of hand-over-hand in a model AAA+ motor, RuvB. To do so, we develop a general method to compute the residue-scale elastic pseudoenergy due to structure changes and apply it to RuvB structures, recently resolved through cryo-EM. This allows us to quantify how progression through RuvBs mechanochemical cycle translates into residue-scale energy transduction. In particular, we find that DNA binding is associated with overcoming a high energy barrier. This is possible through inter-subunit transmission of energy, and ultimately driven by nucleotide exchange. Furthermore, we show how this structure-inferred energetic quantification can be integrated into a non-equilibrium model of AAA+ assembly dynamics, consistent with single-molecule biophysics measurements. Overall, our work elucidates the energetic basis for the hand-over-hand mechanism in RuvBs cycle. Furthermore, it presents a generally applicable methodology for studying the energetics of conformational cycles in other proteins, allowing to quantitatively bridge data from structural biology and single-molecule biophysics. Author SummaryMolecular motors are proteins that transform chemical energy into motion. To do so, they change their shape through a highly organised cycle. How exactly these changes in shape translate into energy transformations that ultimately result in motion is still not fully understood. In our work, we combined tools from structural biology and biophysics to better quantify and model this process. We focused on RuvB, a motor made of six identical parts that work together to move DNA through its central pore. We first tracked how RuvBs shape changes and how much energy these changes involve, and then built a theoretical model that simulates its operational cycle. More broadly, our approach shows how studying protein energetics can connect the perspectives of structural biology and single-molecule biophysics, thus providing new ways to understand how molecular machines work.