Memory effects in a random walk description of protein structure ensembles

Abstract : In this paper we show that ensembles of well-structured and unstructured proteins can be distinguished by borrowing concepts from non-equilibrium statistical mechanics. For this purpose, we represent proteins by two different polymer models and interpret the resulting polymer configurations as random walks of a diffusing particle in space. The first model is the trace of the Cα-atoms along the protein main chain and the second their projections onto the protein axis. The resulting trajectories are subsequently analyzed using the theory of the Generalized Langevin Equation. Velocities are replaced by displacements relating consecutive points on the discrete protein axes and equilibrium ensemble averages by averages over appropriate protein structure ensembles. The resulting displacement autocorrelation functions resemble those of velocity autocorrelation functions of simple liquids and display a minimum, which can be related to the lengths of secondary structure elements. This minimum is clearly more pronounced for well-structured proteins than for unstruc-tured ones and the corresponding memory function displays a slower decay, indicating a stronger "folding memory".
Complete list of metadatas

Cited literature [9 references]  Display  Hide  Download

https://hal.archives-ouvertes.fr/hal-02117662
Contributor : Konrad Hinsen <>
Submitted on : Thursday, May 2, 2019 - 3:03:39 PM
Last modification on : Tuesday, June 18, 2019 - 11:46:02 AM

File

preprint.pdf
Files produced by the author(s)

Identifiers

Citation

Gerald R. Kneller, Konrad Hinsen. Memory effects in a random walk description of protein structure ensembles. Journal of Chemical Physics, American Institute of Physics, 2019, 150 (6), pp.064911. ⟨10.1063/1.5054887⟩. ⟨hal-02117662⟩

Share

Metrics

Record views

30

Files downloads

74