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.
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. bioRxiv 2024.10.10.617682; doi: https://doi.org/10.1101/2024.10.10.617682 (2024)
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)