Coarse-grained simulations of proteins and protein polymers

Principal investigator: Prof. Gregory A. Voth, Dr. Tamara C. Bidone

We harness Brownian dynamics simulations of integrin coarse-grained models to gain insight into the pathway of integrin activation, which is impossible to trace with all-atom molecular dynamics simulations due to its slow nature. Furthermore, we parametrize bottom-up coarse-grained model of a microtubule based on all-atom molecular dynamics simulations and use it to quantify the differences in stability between microtubules with GDP vs. GTP nucleotide in exchangeable binding sites of tubulin monomers.

On the Curvature and Relaxation of Microtubule Plus-end Tips

Skóra T., Wu, J., Beckett, D., Xue, W, Voth, G. A.. & Bidone, T. C. On the Curvature and Relaxation of Microtubule Plus-end Tips. BioRxiv (2025)

Data-Driven Equation-Free Dynamics Applied to Many-Protein Complexes: The Microtubule Tip Relaxation

Wu, J., Dasetty, S., Beckett, D., Wang, Y., Xue, W., Skóra, T., Bidone, T. C., Ferguson, A. L., & Voth, G. A. Data-Driven Equation-Free Dynamics Applied to Many-Protein Complexes: The Microtubule Tip Relaxation. Biophysical Journal (2025)

Contributions of the individual domains of αIIbβ3 integrin to its extension: Insights from multiscale modeling

Skóra, T., Joshi, O., Yarema, A., Rabbitt, R. D., & Bidone, T. C. Contributions of the individual domains of αIIbβ3 integrin to its extension: Insights from multiscale modeling. Cytoskeleton 81, 393-408 (2024)

Bottom-up coarse-grained model of microtubule dynamics: A bridge between length- and timescales

Skóra, T., Beckett, D., & Bidone, T. C. Bottom-up coarse-grained model of microtubule dynamics: A bridge between length- and timescales. Biophysical Journal 123, 272a (2024)