TY - JOUR AU - Hung, Nguyen Ba AU - Hoang, Trinh Xuan PY - 2019/05/14 Y2 - 2024/03/29 TI - Sampling the Folding Transition State Ensemble in a Tube-like Model of Protein JF - Communications in Physics JA - Comm. Phys. VL - 29 IS - 2 SE - Papers DO - 10.15625/0868-3166/29/2/13670 UR - https://vjs.ac.vn/index.php/cip/article/view/13670 SP - 129 AB - <p>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<br />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 umbrella sampling technique. We show that the transition state ensemble is broad consisting of different conformations that have different folded and unfolded elements.</p> ER -