Dresden 2017 – scientific programme

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DY: Fachverband Dynamik und Statistische Physik

DY 3: Computational Biophysics (joint BP/DY)

DY 3.11: Talk

Monday, March 20, 2017, 12:30–12:45, ZEU 250

Characterization of coarse-grained helix-coil transition networks — •Joseph Rudzinski, Kurt Kremer, and Tristan Bereau — Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany

A variety of models, with widely-varying resolution, have contributed to our interpretation of the protein folding process. While atomically-detailed simulations have emerged as an invaluable tool for describing the subtle details which determine particular folding processes, simple physics- and native structure-based coarse-grained (CG) models laid the foundation for current protein folding theories. Despite the success of the latter in describing the essential features of protein folding, the reduced degrees of freedom in CG models inherently obscures the resulting dynamical properties, generally limiting their utility. In this work, we investigate to what extent CG models can describe the precise network of transition pathways for particular protein folding processes. As a model system, we consider the well-studied problem of helix-coil transition kinetics. To elucidate the generic features of the transition, while retaining an accurate description of the transition pathways, we consider a hybrid model with simple, physically-motivated interactions coupled with atomically-detailed sterics. We compare the resulting transition network to networks generated from both an all-atom model and a more sophisticated, transferable CG model. Our results indicate that many features of the transition network are prescribed by rather generic features of the model, motivating further investigation of protein folding kinetics using this approach.