Berlin 2015 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 55: Networks: From Topology to Dynamics II (joint DY/BP/SOE)
BP 55.2: Vortrag
Freitag, 20. März 2015, 09:45–10:00, BH-N 128
Random Networks with Geometric Constraints -- Models for Protein Folding — •Nora Molkenthin1, Antonia S. J. S. Mey3, and Marc Timme1,2 — 1Network Dynamics, Max Planck Institute for Dynamics and Self-Organization, 37077 Göttingen, Germany — 2Institute for Nonlinear Dynamics, Faculty of Physics, University of Göttingen, 37077 Göttingen, Germany — 3Department for Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195 Berlin
How proteins fold crucially underlies their final structure and thus function. Theoretical analyses of protein folding range from full molecular dynamics simulations aimed at modeling the process as accurately as possible, to minimal models to reveal basic physical mechanisms. All existing methods, however, are typically computationally expensive and thus only feasible for relatively short chains of amino acid residues.
Here we introduce a novel dynamical folding model based on random networks with geometric constraints. The protein is modeled as a closed chain of identical spheres, that are connected if they touch each other. New connections are drawn randomly from those potential connections, that do not lead to any spheres intersecting or any existing links having to be broken up. We show that the resulting network is, for instance, akin to protein contact networks (PCN), derived from experimental data using Ca-Atoms as nodes, that are linked if their distance is below 8.5 Angström.
The geometric constraints change the scaling behaviour of the diameter of the network from logarithmic with the number of nodes to a power law, in agreement with that measured in the radius of gyration in real proteins.