Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. I. Six-member, Greek key beta-barrel proteins.
Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. I. Six-member, Greek key beta-barrel proteins.
复制标题
球状蛋白质折叠/展开途径的动态蒙特卡罗模拟。
DOI：
10.1016/0022-2836(90)90237-g
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发表时间：
1990
影响因子：
5.6
通讯作者：
Kolinski,A
中科院分区：
文献类型：
--
作者：
Skolnick,J;Kolinski,A
在拓扑结构与质体蓝素密切相关的六元希腊键 β-桶蛋白的简化钻石晶格模型的背景下，使用动态蒙特卡罗技术研究了折叠和展开路径的性质。希腊琴键组装的机制最好被描述为间断的“现场施工”。折叠通常在β-转角处或附近开始，然后通过使用现有的折叠结构作为随后的三级结构组装到其上的支架来顺序形成β-链。平均而言，β 链倾向于从一个急弯拉到下一个急弯。在四元 β 桶组装完成后，会有一个长时间的停顿，因为包含长环的链的随机卷曲部分会剧烈地尝试寻找自然状态。因此，存在必须克服的熵障碍。然而，虽然蛋白质的某一部分可能正在折叠，但另一部分可能正在展开。因此，存在着在溶解之前组装相当稳定的中间体的竞争。折叠可能在任何急转弯处开始，但由于众所周知的排除体积效应，靠近 N 末端的转弯似乎是首选。当蛋白质第一次开始折叠时，存在多种折叠途径，但随着系统越来越接近天然状态，选择的数量会减少。在早期阶段，已组装的蛋白质所产生的排除体积效应有助于随后的组装。然后，在天然构象附近，折叠部分减少了剩余未折叠部分可利用的构象空间。展开本质上是相反发生的。采用简单的统计力学理论，构建了该模型沿反应坐标的构型自由能。自由能表面与模拟一致，提供了以下预测。过渡态非常接近天然状态，由完全组装的六个 β 链中的五个组成，剩余的长环加上第六条 β 链就位，但仅部分组装。它通过主要是熵起源的自由能势垒与β-桶中间体分开，并通过主要是能量起源的势垒与自然状态分开。后一个特征与戈登堡和克赖顿描述的“纸板箱”模型一致，但与他们的模型不同的是，过渡态不是原生态的高能扭曲形式。该理论预测折叠速率对折叠条件变化的敏感度低于展开速率，这与实验一致。最后，这个简单的理论提供了一种评估有利于类似天然转角形成的氨基酸取代效果的方法。通过稳定中间体，它们提高了从变性状态到中间体的折叠速率和从天然状态展开的速率，并且它们起到减慢从中间体到天然状态的折叠速率的作用。但即使每回合残基都被修改，效果也相对较小。
In the context of a simplified diamond lattice model of a six-member, Greek key β-barrel protein that is closely related in topology to plastocyanin, the nature of the folding and unfolding pathways have been investigated using dynamic Monte Carlo techniques. The mechanism of Greek key assembly is best described as punctuated “on site construction”. Folding typically starts at or near a β-turn, and then the β-strands sequentially form by using existing folded structure as a scaffold onto which subsequent tertiary structure assembles. On average, β-strands tend to zip up from one tight bend to the next. After the four-member, β-barrel assembles, there is a long pause as the random coil portion of the chain containing the long loop thrashes about trying to find the native state. Thus, there is an entropic barrier that must be surmounted. However, while a given piece of the protein may be folding, another section may be unfolding. A competition therefore exists to assemble a fairly stable intermediate before it dissolves. Folding may initiate at any of the tight turns, but the turn closer to the N terminus seems to be preferred due to well-known excluded volume effects. When the protein first starts to fold, there are a multiplicity of folding pathways, but the number of options is reduced as the system gets closer to the native state. In the early stages, the excluded volume effect exerted by the already assembled protein helps subsequent assembly. Then, near the native conformation, the folded parts reduce the accessible conformational space available to the remaining unfolded sections. Unfolding essentially occurs in reverse. Employing a simple statistical mechanical theory, the configurational free energy along the reaction co-ordinate for this model has been constructed. The free energy surface, in agreement with the simulations, provides the following predictions. The transition state is quite near the native state, and consists of five of the six β-strands being fully assembled, with the remaining long loop plus sixth β-strand in place, but only partially assembled. It is separated from the β-barrel intermediate by a free energy barrier of mainly entropic origin and from the native state by a barrier that is primarily energetic in origin. The latter feature is in agreement with the “Cardboard Box” model described by Goldenberg and Creighton but, unlike their model, the transition state is not a high-energy distorted form of the native state. The theory predicts that the rate of folding is less sensitive to changes in folding conditions than is the rate of unfolding, in agreement with experiment. Finally, the simple theory provides a means of assessing the effects of amino acid substitutions that favor native-like turn formation. By stabilizing the intermediate, they enhance the rate of folding to the intermediate from the denatured state and the rate of unfolding out of the native state, and they act to slow down the rate of folding from the intermediate to the native state. But even when every turn residue is modified, the effect is relatively small.