Coarse grained description of the protein folding

TL;DR

This paper simplifies protein folding dynamics into effective state transitions using coarse graining methods, revealing structural features of folding funnels and relating folding times to kinetic traps.

Contribution

It introduces two coarse graining methods for protein folding models and demonstrates their effectiveness in distinguishing good and bad folders through connectivity patterns.

Findings

Connectivity graphs of folding funnels are tree-like with few loops.

Median folding time follows Arrhenius law for 16-monomer sequences.

Folding barriers are linked to kinetic trap states.

Abstract

We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of the effective states. The first method is based on the steepest descent mapping of states to underlying local energy minima and the other involves an additional projection to maximally compact conformations. Both methods generate connectivity patterns that allow to distinguish between the good and bad folders. Connectivity graphs corresponding to the folding funnel have few loops and are thus tree-like. The Arrhenius law for the median folding time of a 16-monomer sequence is established and the corresponding barrier is related to easily identifiable kinetic trap states.