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

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

Content Provider	Springer Nature Link
Author	Duan, LiLi Mei, Ye Li, YongLe Zhang, QingGang Zhang, DaWei Zhang, John ZengHui
Copyright Year	2010
Abstract	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).
Starting Page	196
Ending Page	201
Page Count	6
File Format	PDF
ISSN	16747291
Journal	Science in China Series B: Chemistry
Volume Number	53
Issue Number	1
e-ISSN	18622771
Language	English
Publisher	SP Science in China Press
Publisher Date	2010-02-07
Publisher Place	Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Trp-cage TC5b folding and unfolding replica-exchange melting curve implicit solvation Chemistry/Food Science
Content Type	Text
Resource Type	Article
Subject	Chemistry

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