Stan George, Brooks Bernard R, Thirumalai D
Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
J Mol Biol. 2005 Jul 22;350(4):817-29. doi: 10.1016/j.jmb.2005.05.012.
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 beta-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 Phi 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 alpha-casein (which has no sequence similarity with the apical domain) and the minichaperone and the hydrophobicity profiles we show that alpha-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) alpha-casein-protein complexes. This suggests that alpha-casein assists folding by the TBR mechanism.
虽然在非允许条件下拯救天然底物蛋白（SPs）需要完整的伴侣蛋白机制，但仅包含GroEL分离的顶端结构域的“微型伴侣蛋白”本身就可以协助某一类蛋白质的折叠。为了理解微型伴侣蛋白的退火功能，我们在NPT系综中对四个系统进行了总计300纳秒的分子动力学模拟；即分离的强结合肽（SBP）、微型伴侣蛋白，以及与微型伴侣蛋白结合的SBP和弱结合肽（WBP）。单独存在时无结构的SBP与微型伴侣蛋白结合时会形成β-发夹构象，这表明局限于顶端结构域的H和I螺旋的SPs的有利非特异性相互作用可以诱导局部二级结构。微型伴侣蛋白的游离形式和结合配体形式的动态波动比较表明，稳定性（捕获SPs所必需）涉及SBP和WBP之间以及H和I螺旋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释放涉及H和I螺旋末端带电残基的水介导相互作用。模拟结果与微型伴侣蛋白退火作用的瞬态结合-释放（TBR）模型一致。根据TBR模型，SP退火发生在两个阶段。在第一阶段，SP被顶端结构域捕获。随后是SP释放（通过热涨落），使其处于能量景观的不同区域，从该区域它可以以概率Phi迅速分配到天然状态或被困在另一种错误折叠状态。结合和释放过程可以导致天然状态产率的提高。TBR模型表明“任何能够反复结合和释放SPs的辅因子都可以有效地协助蛋白质折叠”。通过比较非伴侣蛋白α-酪蛋白（与顶端结构域没有序列相似性）和微型伴侣蛋白的结构以及疏水性分布，我们表明α-酪蛋白有一对与H和I具有相似序列和结构分布的螺旋。基于此比较，我们确定了稳定（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。
