How Does a Registry Change in Dynein’s Coiled-Coil Stalk Drive Binding of Dynein to Microtubules?

Abstract

Dynein is a motor protein that transports cellular cargo along the microtubule (MT) by consuming ATP. Dynein's microtubule-binding domain (MTBD) is separated from the ATP-binding core by a ~15 nm stalk that consists of two α-helices forming an antiparallel coiled coil. It was previously suggested that the coiled-coil stalk creates a registry shift to modulate its binding affinity for MT. A crystal structure of the low-affinity form of MTBD was determined, but that of the high-affinity form with the registry shift is not yet available. In this study, we obtained an all-atom model structure for the high-affinity form of MTBD bound to MT by an anisotropic network model, protein-protein docking, and molecular dynamics simulations. We observe that the magnitude of the coiled-coil helix sliding is dramatically reduced near the two prolines that form the stalk-MTBD boundary and subsequently transformed to cyclic movements of MTBD helices, leading to formation of a new salt bridge with MT at the binding interface. The proposed mechanism explains the roles of highly conserved residues such as the two prolines at the stalk-MTBD boundary, the nonpolar tryptophan and proline residues near the binding interface, and the electropositive residues forming salt bridges with MT.

Long-Range Electrostatic Interactions Significantly Modulate the Affinity of Dynein for Microtubules

“…Similar long-range electrostatic interaction-guided regulation mechanisms were reported earlier in the case of kinesin motors (65,66,72). Together with the results from previous experimental work detailing how the short-range electrostatic interactions that constitute surface charge complementarity at the MTBDmicrotubule binding interface (22,29,31) and specific, dynamic salt-bridges within the MTBD (24) underly the microtubule-binding affinity, our results help build a more complete picture of how electrostatics govern the molecular mechanics of dynein motility. We propose that long-range electrostatic interactions, short-range electrostatic interactions, and dynamic salt bridges significantly contribute to various aspects of the binding affinity mechanism as a function of the distance the MTBD is from the microtubule.…”

“…The affinity of dynein for microtubules switches between high-and low-binding affinity states due to conformational changes in the MTBD, which results from changing registrations of the coiled-coil stalk domain helices (19,(23)(24)(25)(26) in response to the ATPase cycle state in AAA1 (19,22,27,28). It is thought that dynein switches to its high-binding affinity state when it is unbound from the microtubule, causing it to bind, and that it switches to its low binding affinity state when it is bound to the microtubule, causing it to unbind and step forward (29,30).…”

“…Electrostatic interactions dominate the dynein-microtubule binding affinity mechanisms. Charged-to-neutral and charge-flipping amino acid substitutions in the MTBD's microtubule-binding interface altered the microtubule-binding affinity (22, 29, 31), presumably due to changes in surface charge complementarity (32, 33). Additionally, multiple dynamic salt-bridges within the MTBD and between the MTBD and the microtubule regulate the MTBD-microtubule-binding affinity (24).…”

Coiled‐coil registry shifts in the F684I mutant of Bicaudal D result in cargo‐independent activation of dynein motility

“…far only been reported for a few proteins, including dynein (Carter et al, 2008;Choi et al, 2011;Croasdale et al, 2011;Gibbons et al, 2005;Kon et al, 2009;Macheboeuf et al, 2011;Noell et al, 2019;Snoberger et al, 2018;Stathopulos et al, 2013;Xi et al, 2012), but may potentially be an inherent property of many coiled-coil structures with important physiological functions. In the case of BicD2, a coiled-coil registry shift may relieve auto-inhibition.…”

The Winch Model Can Explain both Coordinated and Uncoordinated Stepping of Cytoplasmic Dynein

“…The complexity of the dynein molecule and the lack of structural information have also hampered efforts to build a theoretical model describing its dynamics. So far, only a small part of the molecule (the MTBD) has been accessible to molecular dynamics simulations (29). Other studies performed normal mode analysis on a hypothetical ring structure (30) or the stalk coiled-coil (31).…”