Developing Hybrid All-Atom and Ultra-Coarse-Grained Models to Investigate Taxol-Binding and Dynein Interactions on Microtubules

JY Zha and F Xia, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 19, 5621-5632 (2023).

DOI: 10.1021/acs.jctc.3c00275

Simulating the conformations and functions of biologicalmacromoleculesby using all-atom (AA) models is a challenging task due to expensivecomputational costs. One possible strategy to solve this problem isto develop hybrid all-atom and ultra-coarse-grained (AA/UCG) modelsof the biological macromolecules. In the AA/UCG scheme, the interestregions are described by AA models, while the other regions are describedin the UCG representation. In this study, we develop the hybrid AA/UCGmodels and apply them to investigate the conformational changes ofmicrotubule-bound tubulins. The simulation results of the hybrid modelselucidated the mechanism of why the taxol molecules selectively boundmicrotubules but not tubulin dimers. In addition, we also explorethe interactions of the microtubules and dyneins. Our study showsthat the hybrid AA/UCG model has great application potential in studyingthe function of complex biological systems.

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