Berlin 2024 – scientific programme

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BP: Fachverband Biologische Physik

BP 31: Protein Structure and Dynamics

BP 31.8: Talk

Thursday, March 21, 2024, 17:15–17:30, H 0112

Memory-dependent friction in protein folding — •Benjamin Dalton and Roland Netz — Freie Universität Berlin, Fachbereich Physik, Arnimallee 14 14195 Berlin, Germany

When described by a low-dimensional reaction coordinate, the folding rates of many proteins are determined by an interplay between free-energy barriers, which separate folded and unfolded states, and friction. While it is commonplace to extract free-energy profiles from molecular trajectories, a direct evaluation of friction is far more elusive and typically relies on fits of measured reaction rates to memoryless reaction-rate theories. Here, using memory-kernel extraction methods founded on a generalized Langevin equation (GLE) formalism, we directly calculate the time-dependent friction acting on a variety of well-known reaction coordinates for eight fast-folding proteins, taken from a published set of large-scale molecular dynamics protein simulations. We show that memory decay times are typically of the same order as folding times and are much longer than transition-path times. Furthermore, we show that folding times are significantly faster than predictions made by standard Markovian models. This memory-induced reaction speed-up effect is a hallmark of non-Markovian systems, confirming that non-Markovian models are, in general, suitable for describing protein folding dynamics.

Keywords: Protein folding; Memory-dependent friction; non-Markovian; Reaction-rate theory; Molecular dynamics