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BP: Fachverband Biologische Physik
BP 33: Protein Structure and Dynamics
BP 33.9: Vortrag
Donnerstag, 19. März 2020, 12:15–12:30, ZEU 250
Hybrid Kinetic Monte Carlo / Molecular Dynamics Simulations of Bond Scissions in Proteins — •Benedikt Rennekamp1,2 and Frauke Gräter1,2 — 1Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany — 2Interdisciplinary Center for Scientific Computing, Heidelberg University, INF 205, 69120 Heidelberg, Germany
Proteins are exposed to various mechanical loads that can lead to covalent bond scissions even before macroscopic failure occurs. In regular Molecular Dynamics (MD) simulations covalent bonds are, however, predefined and reactions cannot occur. Furthermore, such events rarely take place on MD time scales.
We have developed a hybrid Kinetic Monte Carlo / Molecular Dynamics (KIMMDY) scheme that overcomes the separation of time scales of these processes and drastically increases the accessible time scales for reactive MD simulations. Here, bond rupture rates are calculated in the spirit of a transition state model based on the interatomic distances in the MD simulation and then serve as an input for a Kinetic Monte Carlo step.
With this new technique we investigated bond ruptures in a multi-million atom system of tensed collagen, a structural protein found in skin, bones and tendons. Our simulations show a clear concentration of homolytic bond scissions near chemical crosslinks in collagen. We suggest that these created mechanoradicals are a yet unknown connection converting mechanical into oxidative stress. This application also demonstrates the scalability of our hybrid computational approach.