Probing the "annealing" mechanism of GroEL minichaperone using molecular dynamics simulations.
Probing the "annealing" mechanism of GroEL minichaperone using molecular dynamics simulations.
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DOI：
10.1016/j.jmb.2005.05.012
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发表时间：
2005-07
影响因子：
5.6
通讯作者：
G. Stan;B. Brooks;D. Thirumalai
中科院分区：
文献类型：
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作者：
G. Stan;B. Brooks;D. Thirumalai
尽管在不允许的条件下需要完整的伴侣蛋白机制来拯救天然底物蛋白 (SP)，但仅包含 GroEL 的分离顶端结构域的“微型伴侣”本身就可以帮助折叠某一类蛋白质。为了了解微型伴侣的退火功能，我们在 NPT 系综中对四个系统进行了总计 300ns 的分子动力学模拟；即，分离的强结合肽(SBP)、微型伴侣、以及与微型伴侣复合的SBP和弱结合肽(WBP)。 SBP 孤立无结构，采用与微型伴侣复合的 β-发夹构象，表明仅限于顶端域螺旋 H 和 I 的 SP 的有利非特异性相互作用可以诱导局部二级结构。比较apo和配体形式的微型伴侣表明，稳定性（SP捕获所需）涉及SBP和WBP以及螺旋H和I之间有利的疏水相互作用和氢键网络形成。退火作用所需的SP的释放涉及H和I螺旋末端带电残基的水介导的相互作用。模拟结果与微型伴侣退火作用的瞬时结合释放（TBR）模型一致。根据TBR模型，SP退火分两个阶段进行。在第一阶段，SP 被顶端域捕获。接下来是 SP 释放（通过热波动），将其置于能量景观的不同区域，从中它可以以概率 Φ 快速划分到自然状态或被困在另一个错误折叠状态。结合和释放的过程可以导致天然状态产率的提高。 TBR 模型表明“任何能够重复结合和释放 SP 的辅助因子都可以有效地协助蛋白质折叠。”通过比较非分子伴侣 α-酪蛋白（与顶端结构域没有序列相似性）和微型分子伴侣的结构以及疏水性特征，我们发现 α-酪蛋白具有一对与 H 和 I 具有相似序列和结构特征的螺旋。基于此比较，我们鉴定了稳定（不稳定）α-酪蛋白-蛋白质复合物的残基。这表明 α-酪蛋白通过 TBR 机制协助折叠。
Although the intact chaperonin machinery is needed to rescue natural substrate proteins (SPs) under non-permissive conditions the “minichaperone” alone, containing only the isolated apical domain of GroEL, can assist folding of a certain class of proteins. To understand the annealing function of the minichaperone, we have carried out molecular dynamics simulations in the NPT ensemble totaling 300ns for four systems; namely, the isolated strongly binding peptide (SBP), the minichaperone, and the SBP and a weakly binding peptide (WBP) in complex with the minichaperone. The SBP, which is structureless in isolation, adopts a β-hairpin conformation in complex with the minichaperone suggesting that favorable non-specific interactions of the SPs confined to helices H and I of the apical domains can induce local secondary structures. Comparison of the dynamical fluctuations of the apo and the liganded forms of the minichaperone shows that the stability (needed for SP capture) involves favorable hydrophobic interactions and hydrogen bond network formation between the SBP and WBP, and helices H and I. The release of the SP, which is required for the annealing action, involves water-mediated interactions of the charged residues at the ends of H and I helices. The simulation results are consistent with a transient binding release (TBR) model for the annealing action of the minichaperone. According to the TBR model, SP annealing occurs in two stages. In the first stage the SP is captured by the apical domain. This is followed by SP release (by thermal fluctuations) that places it in a different region of the energy landscape from which it can partition rapidly to the native state with probability Φ or be trapped in another misfolded state. The process of binding and release can result in enhancement of the native state yield. The TBR model suggests “that any cofactor that can repeatedly bind and release SPs can be effective in assisting protein folding.” By comparing the structures of the non-chaperone α-casein (which has no sequence similarity with the apical domain) and the minichaperone and the hydrophobicity profiles we show that α-casein has a pair of helices that have similar sequence and structural profiles as H and I. Based on this comparison we identify residues that stabilize (destabilize) α-casein–protein complexes. This suggests that α-casein assists folding by the TBR mechanism.