Exploring the mechanochemical cycle of dynein motor proteins: structural evidence of crucial intermediates

Dyneins, a class of motor proteins consisting of six AAA+ modules (AAA1-AAA6), convert chemical energy derived from the hydrolysis of ATP into mechanical energy to walk along the microtubule track towards its minus end while accomplishing various cellular tasks including the transportation of various intracellular cargos. In a full mechanochemical cycle, dynein goes through ATP binding induced open to closed state transition of AAA1, hydrolysis of that ATP and closed to open state transition induced by the release of hydrolysed products along with linker remodelling in different nucleotide states. Here we built structure based models (SBMs) to explore the sequence of events of this mechanochemical cycle from structural aspects. Free energy and kinetic simulation approaches on a multi-basin SBM of dynein reveal the following pathways: (1) in the closing pathway, the AAA1 domain first converts to a closed state followed by the movement of the linker and (2) in the opening transition, initially the AAA1 domain partially opens up and then the complete linker movement takes place followed by the complete opening of the AAA1 domain. In the opening transition, we have observed two intermediate states from our simulations where the AAA1 domain is partially opened. However, in one state the linker is at a closed position and in the other the linker is at an open position. The existence of such intermediates (Pi released, ADP bound state) of dynein has been suggested by numerous experimental studies earlier. Finally, we discuss the biological relevance of this sequence of events in terms of processivity and efficiency of the cycle. The current study also shows how the basic principle of protein folding can be extended to understand complex phenomena like the stepping mechanism of motor proteins.