Article,
The inherent structure landscape of a protein
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103 (14): 5279-5284 (April 2006)
DOI: {10.1073/pnas.0600102103}
Abstract
Using the Go model of a real protein, we explore the landscape of its
metastable structures. First, we show how the inherent structure energy
density can be obtained from the probability density determined by
sampling molecular dynamics trajectories and quenching. The analysis of
the inherent structure landscape can characterize the folding
transition. Then we show how thermodynamics of the inherent states can
be established to study the equilibrium properties of proteins. Our
work brings some elements into the current discussion about the protein
dynamical transition. The study uses a simplified model to illustrate
the ideas, but, as the inherent structure landscape is much simpler
than the free energy surface of the protein, it appears to be
accessible for an all-atom model of a small protein, at the expense of
much longer calculations.
