Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity
Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity
复制标题
DOI：
10.1006/jmbi.1999.2591
复制
发表时间：
1999-04-02
影响因子：
5.6
通讯作者：
Thirumalai, D
中科院分区：
文献类型：
--
作者：
Betancourt, MR;Thirumalai, D
大肠杆菌的伴侣蛋白系统GroEL和GroES使某些蛋白质能够在自发折叠非常缓慢的条件下折叠，以与其他非生产性通道（如聚集）竞争。我们用简单的晶格模型研究了groel介导的折叠的可能机制。特别是，我们研究了在受限环境下的蛋白质折叠，例如由GroEL提供的环境，以破译当底物蛋白在伴侣蛋白的空腔内折叠时，是否会发生速率和产量的提高。将GroEL空腔建模为一个立方盒子，并使用一个简单的头模型来表示衬底链。我们考虑了密闭环境的三个不同特征。首先，该空腔被认为是一个被动的安芬森笼，其中的壁只是减少了可用的构象空间。我们发现，在固有构象稳定的温度下，安芬森笼中的折叠速率减慢。然后我们假设壁的内部是疏水的。在这种情况下，折叠时间表现出复杂的行为。当多肽链与空腔之间的相互作用强度过大或过弱时，我们发现与自发折叠相比，折叠速率减慢。存在一个提高速率的最佳相互作用强度范围。因此，在此值以上，折叠率与衬底-腔相互作用的强度呈反比关系。最佳的疏水壁本质上拉动动力学捕获状态，从而导致更平滑的能量景观。众所周知，在加入ATP和GroES后，GroEL的内部空腔为底物蛋白提供了亲水的环境。为了在动态安芬森笼模型的背景下模拟这一点，我们允许改变腔壁的疏水性。在ATP水解的一个周期中，壁保持疏水性的持续时间是允许变化的。这些计算表明，在非允许条件下，频繁的壁疏水性循环可以显著减少折叠次数并提高收率。检查底物蛋白在疏水性变化前后的结构表明，有一个全局展开参与。此外，还发现部分分子根据迭代退火机制在动力学上分拆到原生态。因此，伴侣蛋白频繁的“展开酶”活性导致多肽链的全局展开，从而提高折叠速率和折叠蛋白的产量。我们认为，如果减少循环时间，伴侣蛋白的效率可以大大提高。这些计算被用来解释一些关于伴侣蛋白介导的蛋白质折叠的实验。(C) 1999学术出版社。
The chaperonin system, GroEL and GroES of Escherichia coli enable certain proteins to fold under conditions when spontaneous folding is prohibitively slow as to compete with other non-productive channels such as aggregation. We investigated the plausible mechanisms of GroEL-mediated folding using simple lattice models. In particular, we have investigated protein folding in a confined environment, such as those offered by the GroEL, to decipher whether rate and yield enhancement can occur when the substrate protein is allowed to fold within the cavity of the chaperonins. The GroEL cavity is modeled as a cubic box and a simple bead model is used to represent the substrate chain. We consider three distinct characteristic of the confining environment. First, the cavity is taken to be a passive Anfinsen cage in which the walls merely reduce the available conformation space. We find that at temperatures when the native conformation is stable, the folding rate is retarded in the Anfinsen cage. We then assumed that the interior of the wall is hydrophobic. In this case the folding times exhibit a complex behavior. When the strength of the interaction between the polypeptide chain and the cavity is too strong or too weak we find that the rates of folding are retarded compared to spontaneous folding. There is an optimum range of the interaction strength that enhances the rates. Thus, above this value there is an inverse correlation between the folding rates and the strength of the substrate-cavity interactions. The optimal hydrophobic walls essentially pull the kinetically trapped states which leads to a smoother the energy landscape. It is known that upon addition of ATP and GroES the interior cavity of GroEL offers a hydrophilic-like environment to the substrate protein. In order to mimic this within the context of the dynamic Anfinsen cage model, we allow for changes in the hydrophobicity of the walls of the cavity. The duration for which the walls remain hydrophobic during one cycle of ATP hydrolysis is allowed to vary. These calculations show that frequent cycling of the wall hydrophobicity can dramatically reduce the folding times and increase the yield as well under non-permissive conditions. Examination of the structures of the substrate proteins before and after the change in hydrophobicity indicates that there is global unfolding involved. Ln addition, it is found that a fraction of the molecules kinetically partition to the native state in accordabce with the iterative annealing mechanism. Thus, frequent "unfoldase" activity of chaperonins leading to global unfolding of the polypeptide chain results in enhancement of the folding rates and yield of the folded protein. We suggest that chaperonin efficiency can be greatly enhanced if the cycling time is reduced. The calculations are used to interpret a few experiments on chaperonin-mediated protein folding. (C) 1999 Academic Press.