Short talk:
Dynamic framework for large-scale modeling of biomembranes and flexible peripheral proteins

Mohsen Sadeghi1, Frank Noe1

1Freie Universität Berlin, Berlin, Germany

Membrane-associated peripheral proteins are, among other tasks, responsible for shaping and remodeling biomembranes. The necessary cooperative action of a multitude of curvature-inducing proteins is facilitated by indirect membrane-mediated interactions. Quantitative analysis of the dynamics of a collection of peripheral proteins in a consistent model that incorporates membrane kinetics as well protein flexibility and lateral dynamics is essential in fully describing protein aggregation and membrane remodeling processes. Here, we present our dynamic membrane modeling framework, in simulation setups including varying concentrations of flexible membrane-bound proteins. We present quantitative results on membrane-mediated interactions and investigate the aggregation kinetics, stationary distributions, and free energy landscapes governing the formation and break-up of protein clusters on the surface of the membrane. We demonstrate how protein flexibility plays a significant role in highly selective macroscopic aggregation behavior. Relying on transition-based reweighting analysis method (TRAM), we obtain accurate estimates of membrane entropy, and discuss how the balance between entropic and enthalpic forces in protein cluster formation shifts with surface concentration.

1. Sadeghi, Soft Matter (2022) 18.
2. Sadeghi, Noé, J. Phys. Chem. Lett. (2021) 12.
3. Sadeghi, Noé, Nat. Commun. (2020) 11.
4. Sadeghi, Noé, J. Chem. Phys. (2021) 155.
5. Sadeghi, Weikl, Noé, J. Chem. Phys. (2018) 148.

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