Open AccessSampling the Folding Transition State Ensemble in a Tube-Like Model of Protein
Author(s) -
Ba Hung Nguyen,
Hoang Trinh Xuan
Publication year - 2020
Publication title -
kalpa publications in engineering
Language(s) - English
Resource type - Conference proceedings
ISSN - 2515-1770
DOI - 10.29007/ml3c
Subject(s) - protein folding , saddle point , folding (dsp implementation) , energy landscape , native state , downhill folding , phi value analysis , crystallography , saddle , state (computer science) , physics , chemistry , chemical physics , thermodynamics , geometry , mathematics , algorithm , nuclear magnetic resonance , mathematical optimization , electrical engineering , engineering
We used the tube model with Go-like potential for native contacts to study the folding transition of a designed three-helix bundle and a designed protein G-like structure. It is shown that both proteins in this model are two-state folders with a cooperative folding transition coincided with the collapse transition. We defined the transition states as protein conformations in a small region around the saddle point on a free energy surface with the energy and the conformational root-mean-square deviation (RMSD) from the native state as the coordinates. The transition state region on the free energy surface then was sampled by using the umbrella sampling technique. We show that the transition state ensemble is broad consisting of different conformations that have different folded and unfolded elements.