SMBp Group Meeting: Abhilash Sahoo (CCB)

Tuesday Aug 15, 2023, 2:00 PM → 3:00 PM America/New_York

3rd Floor Classroom/3-Flatiron Institute (162 5th Avenue)

Speaker: Abhilash Sahoo (CCB)

 

Topic: Exploring microtubule biophysics with multiscale molecular dynamics simulations

 

Abstract: Microtubules are essential cytoskeletal filaments involved in cell motility, division, and intracellular transport. These biomolecular assemblies can exhibit complex structural behaviors influenced by various biophysical factors. However, simulating microtubule systems at the atomistic scale is challenging due to their large spatial scales. Here, we present an approach utilizing the MARTINI 3 Coarse-Grained (CG) model coupled with an appropriate elastic network to simulate microtubule-based systems accurately. By iteratively optimizing the elastic network parameters, we matched the structural fluctuations of CG hetero-dimer building blocks to their atomistic counterparts. Our aim is to employ these CG simulations to investigate specific biophysical phenomena at a microscopic level. Specifically, we intend to explore the influence of disordered tubulin tails and local salt concentration on crowding-driven microtubule bundling. Additionally, we aim to investigate the impact of local salt concentration on the diffusion behavior of microtubule binding proteins. These microscopic perspectives can provide valuable insights into the underlying mechanisms and contribute to our knowledge of microtubule-associated processes in cellular biology. With MARTINI 3 CG simulations, we can bridge the gap between computational efficiency and molecular detail, enabling investigations into these biophysical processes over longer spatio-temporal scales with amino acid-level insights.