scholarly journals Toward Identification of the Reaction Coordinate Directly from the Transition State Ensemble Using the Kernel PCA Method

2011 ◽  
Vol 115 (10) ◽  
pp. 2465-2469 ◽  
Author(s):  
Dimitri Antoniou ◽  
Steven D. Schwartz
Keyword(s):  
Transition State ◽  
Reaction Coordinate ◽  
Kernel Pca ◽  
State Ensemble ◽  
Pca Method ◽  
Transition State Ensemble

scholarly journals Constrained proper sampling of conformations of transition state ensemble of protein folding

2011 ◽  
Vol 134 (7) ◽  
pp. 075103 ◽  
Author(s):  
Ming Lin ◽  
Jian Zhang ◽  
Hsiao-Mei Lu ◽  
Rong Chen ◽  
Jie Liang
Keyword(s):  
Protein Folding ◽  
Transition State ◽  
State Ensemble ◽  
Transition State Ensemble ◽  
Proper Sampling

scholarly journals Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble

PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0144067 ◽  
Author(s):  
Kaitlin M. Fisher ◽  
Ellinor Haglund ◽  
Jeffrey K. Noel ◽  
Kendra L. Hailey ◽  
José N. Onuchic ◽  
...  
Keyword(s):  
Transition State ◽  
Functional Element ◽  
Geometrical Frustration ◽  
Interleukin 33 ◽  
State Ensemble ◽  
Transition State Ensemble

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

10.29007/ml3c ◽  
2020 ◽  
Author(s):  
Ba Hung Nguyen ◽  
Hoang Trinh Xuan
Keyword(s):  
Free Energy ◽  
Transition State ◽  
Energy Surface ◽  
Sampling Technique ◽  
Small Region ◽  
Umbrella Sampling ◽  
Free Energy Surface ◽  
State Ensemble ◽  
State Region ◽  
Transition State Ensemble

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.

Transition-state Ensemble in Enzyme Catalysis: Possibility, Reality, or Necessity?

2000 ◽  
Vol 203 (4) ◽  
pp. 383-397 ◽  
Author(s):  
BUYONG MA ◽  
SANDEEP KUMAR ◽  
CHUNG-JUNG TSAI ◽  
ZENGJIAN HU ◽  
RUTH NUSSINOV
Keyword(s):  
Transition State ◽  
Enzyme Catalysis ◽  
State Ensemble ◽  
Transition State Ensemble

scholarly journals Protein folding funnels: the nature of the transition state ensemble

1996 ◽  
Vol 1 (6) ◽  
pp. 441-450 ◽  
Author(s):  
José Nelson Onuchic ◽  
Nicholas D. Socci ◽  
Zaida Luthey-Schulten ◽  
Peter G. Wolynes
Keyword(s):  
Protein Folding ◽  
Transition State ◽  
State Ensemble ◽  
Transition State Ensemble
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