ct300878a_si_001.pdf (563.92 kB)
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
journal contribution
posted on 2013-04-09, 00:00 authored by Christian
R. Schwantes, Vijay S. PandeMarkov
State Models (MSMs) provide an automated framework to investigate
the dynamical properties of high-dimensional molecular simulations.
These models can provide a human-comprehensible picture of the underlying
process and have been successfully used to study protein folding,
protein aggregation, protein ligand binding, and other biophysical
systems. The MSM requires the construction of a discrete state-space
such that two points are in the same state if they can interconvert
rapidly. In the following, we suggest an improved method, which utilizes
second order Independent Component Analysis (also known as time-structure
based Independent Component Analysis, or tICA), to construct the state-space.
We apply this method to simulations of NTL9 (provided by Lindorff-Larsen
et al. Science 2011, 334, 517–520) and show that the MSM is an improvement over previously
built models using conventional distance metrics. Additionally, the
resulting model provides insight into the role of non-native contacts
by revealing many slow time scales associated with compact, non-native
states.