Simulation of the thermodynamics of folding and unfolding of the Trp-cage mini-protein TC5b using different combinations of force fields and solvation models  

作　　者：ZHANG John ZengHui 

机构地区：[1]State Key Laboratory of Precision Spectroscopy,Department of Physics,East China Normal University [2]Department of Chemistry,New York University,New York,New York 10003,USA

出　　处：《Science China Chemistry》2010年第1期196-201,共6页中国科学（化学英文版）

基　　金：supported by the National Basic Research Program of China (Grant No. 2004CB719901);the National Natural Science Foundation of China (Grants No.10874104,20773060);the Natural Science Foundation of Shandong Province (Grant No.Z2007A05)

摘　　要：Molecular dynamics simulations based on AMBER force fields(ff96 and ff03) and generalized Born models(igb1 and igb5) have been carried out in order to study folding/unfolding of the Trp-cage mini-protein TC5b.The thermodynamic properties of TC5b were found to be sensitive to the specific version of the solvation model and force field employed.When the ff96/igb5 combination was used,the predicted melting temperature from unfolding simulations was in good agreement with the experimental value of 315 K,but the folding simulation did not converge.The most stable thermodynamic profile in both folding and unfolding simulations was obtained when the ff03/igb5 combination was employed,and the predicted melting temperature was about 345 K,showing over-stabilization of the protein.Simulations using the igb1 version in combination with ff96 or ff03 were difficult to converge within the simulation time limit(50 ns).Molecular dynamics simulations based on AMBER force fields(ff96 and ff03) and generalized Born models(igb1 and igb5) have been carried out in order to study folding/unfolding of the Trp-cage mini-protein TC5b.The thermodynamic properties of TC5b were found to be sensitive to the specific version of the solvation model and force field employed.When the ff96/igb5 combination was used,the predicted melting temperature from unfolding simulations was in good agreement with the experimental value of 315 K,but the folding simulation did not converge.The most stable thermodynamic profile in both folding and unfolding simulations was obtained when the ff03/igb5 combination was employed,and the predicted melting temperature was about 345 K,showing over-stabilization of the protein.Simulations using the igb1 version in combination with ff96 or ff03 were difficult to converge within the simulation time limit(50 ns).

关 键 词：TRP-CAGE TC5b FOLDING and UNFOLDING REPLICA-EXCHANGE melting curve implicit SOLVATION 

分 类 号：Q51[生物学—生物化学]