Sampling the Folding Transition State Ensemble in a Tube-Like Model of Protein

10 pages•Published: May 14, 2020

Abstract

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.

Keyphrases: computational physics, folding transition, go like potential, root mean square deviation, tube like model

In: Tich Thien Truong, Trung Nghia Tran, Quoc Khai Le and Thanh Nha Nguyen (editors). Proceedings of International Symposium on Applied Science 2019, vol 3, pages 197-206.

Links:	https://easychair.org/publications/paper/8HpP
	https://doi.org/10.29007/ml3c

BibTeX entry

@inproceedings{ISAS2019:Sampling_Folding_Transition_State,
  author    = {Ba Hung Nguyen and Hoang Trinh Xuan},
  title     = {Sampling the Folding Transition State Ensemble in a Tube-Like Model of Protein},
  booktitle = {Proceedings of International Symposium on Applied Science 2019},
  editor    = {Tich Thien Truong and Trung Nghia Tran and Quoc Khai Le and Thanh Nha Nguyen},
  series    = {Kalpa Publications in Engineering},
  volume    = {3},
  publisher = {EasyChair},
  bibsource = {EasyChair, https://easychair.org},
  issn      = {2515-1770},
  url       = {/publications/paper/8HpP},
  doi       = {10.29007/ml3c},
  pages     = {197-206},
  year      = {2020}}

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