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BP: Fachverband Biologische Physik

BP 12: Computational Biophysics I

BP 12.4: Vortrag

Dienstag, 13. März 2018, 10:15–10:30, H 1058

Structural-kinetic relationships determine consistent interpretations of coarse-grained peptide kinetics — •Joseph Rudzinski and Tristan Bereau — Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz

Coarse-grained molecular simulation models have provided tremendous insight into the complex behavior of protein systems, but lack a straightforward connection to the true dynamical properties of the system. This lack of consistent dynamics severely limits coarse-grained models from providing accurate interpretations for kinetic experiments. In this work, we perform a detailed investigation into the kinetic properties of secondary structure formation generated by molecular simulation models. Our strategy is to systematically vary force-field parameters of a simple, native-biased coarse-grained model to identify relationships between the emergent structural, kinetic, and thermodynamics properties. We utilize Markov state models to efficiently and systematically assess the system's kinetic properties. Our investigation reveals robust structural-kinetic relationships that can be exploited to guarantee consistent kinetics through the reproduction of particular structural properties. These remarkable relationships are determined by the physics of the model, which shapes the free-energy landscape and restricts the attainable kinetic properties. Our results suggest an approach for constructing kinetically-accurate models that extends the capabilities and scope of current coarse-grained peptide models.