Dresden 2020 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 33: Protein Structure and Dynamics

BP 33.7: Vortrag

Donnerstag, 19. März 2020, 11:45–12:00, ZEU 250

Investigating the conformational ensembles of intrinsically-disordered proteins with a simple physics-based model — •Yani Zhao, Robinson Cortes-Huerto, Kurt Kremer, and Joseph F. Rudzinski — Max Planck Institute for Polymer Research, Mainz, Germany

The coupled interactions of intrinsically disordered proteins (IDPs) with its partners play an important role in biological processes but present a number of fundamental challenges for computational modeling. This challenge is magnified for proteins due to the variety of competing interactions and large deviations in side-chain properties. In this work, we apply a simple physics-based coarse-grained model for describing largely disordered conformational ensembles of peptides, based on the premise that sampling sterically-forbidden conformations can compromise the faithful description of both static and dynamical properties. The Hamiltonian of the employed model can be easily adjusted to investigate the impact of distinct interactions and sequence specificity on the randomness of the resulting conformational ensemble. Starting with a bead-spring-like model and then adding more detailed interactions one by one, we construct a hierarchical set of models and perform a detailed comparison of their properties. Our analysis clarifies the role of generic attractions, electrostatics and side-chain sterics, while providing a foundation for developing efficient models for IDPs that retain an accurate description of the hierarchy of conformational dynamics, which is nontrivially influenced by interactions with surrounding proteins and solvents.