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Designability, thermodynamic stability, and dynamics in protein folding: a lattice model study

Régis Mélin·Hao Li·Ned S. Wingreen·Chao Tang
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Abstract

In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against mutating the amino-acid sequence, and must be fast folders. We find two criteria which, together, guarantee that a sequence will be ``protein like'': i) the ground state is a highly designable stucture, i. e. the native structure is the ground state of a large number of sequences, and ii) the sequence has a large $Δ/Γ$ ratio, $Δ$ being the average energy separation between the ground state and the excited compact conformations, and $Γ$ the dispersion in energy of excited compact conformations. These two criteria are not incompatible since, on average, sequences whose ground states are highly designable structures have large $Δ/Γ$ values. These two criteria require knowledge only of the compact-state spectrum. These claims are substantiated by the study of 45 sequences, with various values of $Δ/Γ$ and various degrees of designability, by means of a Borst-Kalos-Lebowitz algorithm, and the Ferrenberg-Swendsen histogram optimization method. Finally, we report on the reasons for slow folding. A comparison between a very slow folding sequence, an average folding one and a fast folding one suggests that slow folding originates from a proliferation of nearly compact low-energy conformations, not present for fast folders.

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Régis Mélin, Hao Li, Ned S. Wingreen, Chao Tang. 1998-06-16. Designability, thermodynamic stability, and dynamics in protein folding: a lattice model study. https://doi.org/10.1063/1.478168

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