ci9b00942_si_001.pdf (4.8 MB)
Protein Dynamics and the Folding Degree
journal contribution
posted on 2020-02-21, 22:43 authored by Vladimir Sladek, Ryuhei Harada, Yasuteru ShigetaThe analysis of folding
trajectories for proteins is an open challenge.
One of the problems is how to describe the amount of folded secondary
structure in a protein. We extend the use of Estradas’ folding
degree (Bioinformatics 2002, 18, 697) for the analysis of the evolution of the folding
stage during molecular dynamics (MD) simulation. It is shown that
residue contribution to the total folding degree is a predominantly
local property, well-defined by the backbone dihedral angles at the
given residue, without significant contribution from the backbone
conformation of other residues. Moreover, the magnitude of this residue
contribution can be quite easily associated with characteristic motifs
of secondary protein structures such as the α-helix, β-sheet
(hairpin), and so on by means of a Ramachandran-like plot as a function
of backbone dihedral angles φ,ψ. Additionally, the understanding
of the free energy profile associated with the folding process becomes
much simpler. Often a 1D profile is sufficient to locate global minima
and the corresponding structure for short peptides.