Molecular dynamics of folding of secondary structures in Go-type models of proteins

TL;DR

This study uses molecular dynamics simulations of Go-type models to analyze the folding mechanisms, stability, and vibrational properties of various protein secondary structures, revealing insights into folding sequences and effects of constraints.

Contribution

It introduces detailed off-lattice Go-type models with and without steric constraints, providing new insights into folding pathways, stability, and vibrational spectra of protein secondary structures.

Findings

Models with steric constraints are better folders and more stable.

Folding proceeds through a sequence of events specific to each structure.

Folding times depend linearly on viscous friction in a moderate regime.

Abstract

We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and a soft repulsion for the non-native contacts. The interactions are chosen to make the target secondary structure be the native state of the system. We provide a thorough equilibrium and kinetic characterization of the sequences through the molecular dynamics simulations with the Langevin noise. Models with the steric constraints are found to be better folders and to be more stable, especially in the case of the $\beta$-structures. Phononic spectra for vibrations around the native states have low frequency gaps that correlate with the thermodynamic stability. Folding of the secondary structures proceeds through a well defined sequence of events. For instance, $\alpha$-helices fold from the ends first. The closer to the native state, the faster establishment of the contacts. Increasing the system size deteriorates the folding characteristics. We study the folding times as a function of viscous friction and find a regime of moderate friction with the linear dependence. We also consider folding when one end of a structure is pinned which imitates instantaneous conditions when a protein is being synthesized. We find that, under such circumstances, folding of helices is faster and of the $\beta$-sequences slower.