Application of temperature replica exchange molecular dynamics: Structure of mitotic spindle-associated protein SHE1 and its binding to dynein

Cytoskeletal motor protein dynein belongs to the AAA+ superfamily of enzymes, functioning as a mechanochemical ATPase that converts chemical energy into force to drive its retrograde movements along microtubules. Dynein is responsible for cellular cargo transportation; however, viral particles can also recruit dynein. Dynein's mutation is also critical in neurodegenerative and neurodevelopmental diseases. SHE1 is a yeast-specific MT-associated protein that promotes polarizing dynein-mediated spindle movements. Unlike dynein's adaptor proteins, SHE1 is the only protein known to inhibit dynein motility, act independently from dynactin, and alter dynein activity. Despite SHE1's unique mode of action, its structure has not yet been solved experimentally. This work presents the SHE1 structure obtained using Temperature Replica Exchange Molecular Dynamics simulations. The resulting structure was used to explore the conformations of the complex formed by SHE1 binding to dynein and/or microtubule. The conformations of the complex obtained from the computational protein-protein binding study were clustered using the unsupervised machine learning K-means algorithm. The results helped identify the potential SHE1-dynein interaction sites and the participating amino acids, as well as explaining the structural details underlying SHE1's potential inhibitory mechanisms. In one of the two main recognized binding sites of SHE1 in the SHE1-dynein complexes, its inhibitory mechanism can be due to its interference with the long-range allosteric communications of dynein's domains, namely strut-stalk-MTBD. In that binding mode, SHE1 can restrain the AAA1/AAA4 modules of the motor ring, affecting its "open-closed" conformational changes. That suggests SHE1 could directly interfere with the ATP-hydrolyzing modules necessary for dynein motility. In the second observed binding site, SHE1 interacts with MTBD, α-tubulin, and the C-terminal tail of β-tubulin (E-hook) thereby inhibiting the high binding affinity mode of MTBD to microtubules preventing its motility, which aligns with recent <i>in vitro</i> experimental data. Characterizing the SHE1 structure and its complex with SHE1-dynein can aid in the design and development of therapeutic peptide inhibitors of dynein or its mutants for treating dynein-involved diseases.