Study of multiple unfolding trajectories and unfolded states of the protein GB1 under the physical property space.
Forty nine molecular dynamics simulations of unfolding trajectories of the segment B1 of streptococcal protein G (GB1) provide a direct demonstration of the diversity of unfolding pathway and give a statistically utmost unfolding pathway under the physical property space. Twelve physical properties of the protein were chosen to construct a 12-dimensional property space. Then the 12-dimensional property space was reduced to a 3-dimensional principle component property space. Under the property space, the multiple unfolding trajectories look like "trees", which have some common characters. The "root of the tree" corresponds to the native state, the "bole" homologizes the partially unfolded conformations, and the "crown" is in correspondence to the unfolded state. These unfolding trajectories can be divided into three types. The first one has the characters of straight "bole" and "crown" corresponding to a fast two-state unfolding pathway of GB1. The second one has the character of "the standstill in the middle tree bole", which may correspond to a three-state unfolding pathway. The third one has the character of "the circuitous bole" corresponding to a slow two-state unfolding pathway. The fast two-state unfolding pathway is a statistically utmost unfolding pathway or preferred pathway of GB1, which occupies 53% of 49 unfolding trajectories. In the property space all the unfolding trajectories construct a thermal unfolding pathway ensemble of GB1. The unfolding pathway ensemble resembles a funnel that is gradually emanative from the native state ensemble to the unfolded state ensemble. In the property space, the thermal unfolded state distribution looks like electronic cloud in quantum mechanics. The unfolded states of the independent unfolding simulation trajectories have substantial overlaps, indicating that the thermal unfolded states are confined by the physical property values, and the number of protein unfolded state are much less than that was believed before.
Wang
Jihua
J
Key Laboratory for Biophysics of Shandong Province and Physics, Department of De Zhou University, 253023, De Zhou, Shandong, China. jhwyh@yahoo.com.cn
Zhao
Liling
L
Dou
Xianghua
X
Zhang
Zhiyong
Z
D001426:Bacterial Proteins / Q000737:chemistry; D019295:Computational Biology; D011487:Protein Conformation; D017510:Protein Folding; D013816:Thermodynamics
D001426:Bacterial Proteins; C034284:IgG Fc-binding protein, Streptococcus