1. Fast protein folding is governed by memory-dependent friction.
- Author
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Dalton, Benjamin A., Ayaz, Cihan, Kiefer, Henrik, Klimek, Anton, Tepper, Lucas, and Netz, Roland R.
- Subjects
PROTEIN folding ,FRICTION ,LANGEVIN equations ,MOLECULAR dynamics - Abstract
When described by a low-dimensional reaction coordinate, the folding rates of most proteins are determined by a subtle 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 reactionrate theories. Here, using memory-kernel extraction methods founded on a generalized Langevin equation (GLE) formalism, we directly calculate the time-dependent friction acting on the fraction of native contacts reaction coordinateQ, evaluated for eight fastfolding proteins, taken from a published set of large-scale molecular dynamics protein simulations. Our results reveal that, across the diverse range of proteins represented in this dataset, friction is more influential than free-energy barriers in determining protein folding rates. We also show that proteins fold in a regime where the finite decay time of friction significantly reduces the folding times, in some instances by as much as a factor of 10, compared to predictions based on memoryless friction. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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