Quasiequilibrium unfolding thermodynamics of a small protein studied by molecular dynamics simulation with an explicit water model.
The 124 independent molecular dynamics simulations are completed with total time of 196.8 ns. The calculated unfolding quasiequilibrium thermodynamics of G-IgG-binding domain B1 (GB1) shows the experimentally observed protein transitions: a coil to disordered globule transition, a disordered globule to molten globule transition, a molten globule to nativelike transition, and a nativelike to solidlike state transition. The first protein unfolding phase diagram has been constructed from molecular dynamics simulations with an explicit water model. The calculated melting temperature of GB1 agrees with early experiment. The results also agree with the recent experiment result in which GB1 has more than one intermediate.
Wang
Jihua
J
Department of Physics, De zhou University, De zhou, Shandong, People's Republic of China. jhwyh@yahoo.com.cn
Zhang
Zhiyong
Z
Liu
Haiyan
H
Shi
Yunyu
Y
D001426:Bacterial Proteins / Q000737:chemistry*; D003198:Computer Simulation; D006358:Hot Temperature; D007074:Immunoglobulin G / Q000737:chemistry; D008958:Models, Molecular; D015233:Models, Statistical; D011312:Pressure; D011485:Protein Binding; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors; D014867:Water / Q000737:chemistry*
D001426:Bacterial Proteins; C034284:IgG Fc-binding protein, Streptococcus; D007074:Immunoglobulin G; D011506:Proteins; D014867:Water