Folding of EK peptide and its dependence on salt concentration and pH： A computational study

In this study, we apply both palrwise AMBER03 force field and the recently developed polarized force field to study the folding process of EK peptide under various ion strength and pH conditions. The polarized force field is based on our newly proposed adaptive hydrogen bond-specific charge （AHBC） s...

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Bibliographic Details
Published in:Science China. Chemistry 2011-12, Vol.54 (12), p.1974-1981
Main Authors: Mei, Ye, Zhang, DaWei, Duan, LiLi, Zhang, QingGang, Zhang, John ZengHui
Format: Article
Language:English
Subjects:
Chemistry
Chemistry and Materials Science
Chemistry/Food Science
Folding
Hydrogen bonds
Peptides
pH值
Polarization
Qualitative analysis
Residues
Solvent effect
Structural stability
折叠过程
极化效应
浓度
盐桥
稳定计算
螺旋结构
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Summary:In this study, we apply both palrwise AMBER03 force field and the recently developed polarized force field to study the folding process of EK peptide under various ion strength and pH conditions. The polarized force field is based on our newly proposed adaptive hydrogen bond-specific charge （AHBC） scheme. These two force fields differ only by the atomic charges. Solvent effect is described with generalized Born models （IGB5 in AMBER 10 package）. The result shows that although when applying AMBER03 charge, the helical structure is preferred, its dependence on salt concentration and pH is qualitatively wrong. While using AHBC the peptide finds its native structure within 10 ns, and then fluctuates around this folded state. Under high salt concentration or extreme pH conditions the calculated helical structure probability drops, which is in qualitative agreement with the experiment. Analysis of the atomic charges and the interaction between the donor-acceptor pair in main hydrogen bonds shows that the helical structure is stabilized when polarization effect is counted. It again shows that polarization effect is a very important improvement over traditional force field and is essential for protein folding. We also prove that the salt bridge interaction between 4-residue apart GLU and LYS residues is not critical to the stability of helical structure of EK peptide, but is merely an auxiliary factor, also in agreement with the experiment.
ISSN:1674-7291
1869-1870
DOI:10.1007/s11426-011-4399-3