The inherent structure landscape of a protein.
Using the Gō 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.
Nakagawa
Naoko
N
Department of Mathematical Sciences, Ibaraki University, Mito, Ibaraki 310-8512, Japan. nah@mx.ibaraki.ac.jp
Peyrard
Michel
M
D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins