title: Coarse-Grained Simulations of Protein Backbone Dynamics. 1. Local Sterics Define the Dihedral Angles.
abstract: Here, we present a coarse-grained model targeted for implicit solvent simulations of unfolded or intrinsically disordered proteins. The hierarchical model with its nonspherical building blocks allows one to reproduce the local dynamics of the backbone with simple harmonic bonds and steric collisions between a small number of atoms at the correct off-center positions on the building blocks. Here in part 1, we also describe the implementation of the global shape of the protein chain and the extended local interactions that add a first secondary structure bias, which will subsequently be augmented by additional hydrophobic interactions, hydrogen bonds, and dipole dipole couplings along the backbone. Due to its hierarchical setup, the model has a near-atomistic resolution on the local scale and the overall numerical efficiency of a coarse-grained model such that even long protein chains can be simulated efficiently.
authors.affiliation: Zentrum für Bioinformatik, Universität des Saarlandes, D-66041 Saarbrücken, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Wagenmann
authors.affiliation: Zentrum für Bioinformatik, Universität des Saarlandes, D-66041 Saarbrücken, Germany.
authors.forename: Tihamér
authors.initials: T
authors.lastname: Geyer