Molecular dynamics studies of 尾-hairpin folding with the presence of the sodium ion

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• 作者：Xiaomin Wu^a ; ^b ; Gang Yang^a ; ^c ; ^{theobiochem@gmail.com} ; Yuangang Zu^a ; Lijun Zhou^a
• 关键词：Metal ions ; Molecular dynamics ; Protein folding ; Native H-bonds ; Solvent effects
• 刊名：Computational Biology and Chemistry
• 出版年：2012
• 期刊代码：120_14769271
• 类别：ch
• 出版时间：June, 2012
• 卷：38
• 期：Complete
• 页码：1-9
• 文件大小：1775 K

摘要

Metal ions are ubiquitous in protein systems and play a significant role during their folding processes. Nineteen independent structures were determined for the Na⁺/尾-hairpin interacting systems, and their folding pathways are different. (i) For Na^S47, the turn is rapidly shaped with the help of Na⁺ and acts as the folding nucleus for the rest regions. Two intermediate states are observed and the resulted structure is the most folded. (ii) For Na^B41, Na^B52, Na^B54, Na^S55 and Na^B56, the inclusive Na⁺ ions are anchored by 尾-strands. The local structures around the Na⁺ ions and the turn regions fold simultaneously and serve as two independent folding nuclei. (iii) The other systems have no folding nuclei and correspond to low-folded structures. Long-range electrostatic interactions contribute a lot to the folding, especially from the four negatively charged residues (Glu42, Asp46, Asp47 and Glu56). The initial positions of the Na⁺ ions are largely responsible for the different folding behaviors. The interactions with sidechain- rather than backbone-O atoms generally lead to more compact structures. Another factor affecting the folding is whether the O atoms are associated with native H-bonds, and those involved show decreased affinities to metal ions. The addition of water solvent does not induce obvious folding and conformational transitions to the Na⁺/尾-hairpin interacting systems.