Strenic LLC, McLean, VA, 22102, USA.
, McLean, USA.
Biol Direct. 2018 Jul 6;13(1):13. doi: 10.1186/s13062-018-0217-6.
A half century of studying protein folding in vitro and modeling it in silico has not provided us with a reliable computational method to predict the native conformations of proteins de novo, let alone identify the intermediates on their folding pathways. In this Opinion article, we suggest that the reason for this impasse is the over-reliance on current physical models of protein folding that are based on the assumption that proteins are able to fold spontaneously without assistance. These models arose from studies conducted in vitro on a biased sample of smaller, easier-to-isolate proteins, whose native structures appear to be thermodynamically stable. Meanwhile, the vast empirical data on the majority of larger proteins suggests that once these proteins are completely denatured in vitro, they cannot fold into native conformations without assistance. Moreover, they tend to lose their native conformations spontaneously and irreversibly in vitro, and therefore such conformations must be metastable. We propose a model of protein folding that is based on the notion that the folding of all proteins in the cell is mediated by the actions of the "protein folding machine" that includes the ribosome, various chaperones, and other components involved in co-translational or post-translational formation, maintenance and repair of protein native conformations in vivo. The most important and universal component of the protein folding machine consists of the ribosome in complex with the welcoming committee chaperones. The concerted actions of molecular machinery in the ribosome peptidyl transferase center, in the exit tunnel, and at the surface of the ribosome result in the application of mechanical and other forces to the nascent peptide, reducing its conformational entropy and possibly creating strain in the peptide backbone. The resulting high-energy conformation of the nascent peptide allows it to fold very fast and to overcome high kinetic barriers along the folding pathway. The early folding intermediates in vivo are stabilized by interactions with the ribosome and welcoming committee chaperones and would not be able to exist in vitro in the absence of such cellular components. In vitro experiments that unfold proteins by heat or chemical treatment produce denaturation ensembles that are very different from folding intermediates in vivo and therefore have very limited use in reconstructing the in vivo folding pathways. We conclude that computational modeling of protein folding should deemphasize the notion of unassisted thermodynamically controlled folding, and should focus instead on the step-by-step reverse engineering of the folding process as it actually occurs in vivo.
This article was reviewed by Eugene Koonin and Frank Eisenhaber.
体外研究蛋白质折叠和计算机模拟已有半个世纪，但我们仍没有得到一种可靠的计算方法来预测蛋白质的天然构象，更不用说识别其折叠途径中的中间产物了。在这篇观点文章中，我们认为造成这种僵局的原因是过度依赖目前基于蛋白质能够在没有辅助的情况下自发折叠这一假设的蛋白质折叠物理模型。这些模型源自于在体外对较小、较容易分离的蛋白质进行的偏向性研究，这些蛋白质的天然结构似乎在热力学上是稳定的。同时，关于大多数较大蛋白质的大量经验数据表明，一旦这些蛋白质在体外完全变性，它们就不能在没有辅助的情况下折叠成天然构象。此外，它们在体外往往会自发和不可逆转地失去天然构象，因此这些构象必须是亚稳态的。我们提出了一种蛋白质折叠模型，该模型基于以下观点，即细胞中所有蛋白质的折叠都是由“蛋白质折叠机器”介导的，该机器包括核糖体、各种伴侣蛋白以及其他参与共翻译或翻译后形成、维持和修复蛋白质天然构象的组成部分。蛋白质折叠机器最重要和最普遍的组成部分是与欢迎委员会伴侣蛋白结合的核糖体。核糖体肽基转移酶中心、出口隧道和核糖体表面的分子机制的协同作用导致机械力和其他力施加到新生肽上，降低其构象熵，并可能使肽骨架产生应变。新生肽的这种高能量构象使其能够非常快速地折叠，并克服折叠途径中的高动力学障碍。体内早期折叠中间体通过与核糖体和欢迎委员会伴侣蛋白的相互作用而稳定，如果没有这些细胞成分，它们将无法在体外存在。通过加热或化学处理使蛋白质变性的体外实验产生的变性混合物与体内折叠中间体非常不同，因此在重建体内折叠途径方面的用途非常有限。我们得出结论，蛋白质折叠的计算建模应淡化无辅助热力学控制折叠的概念，而应将重点放在实际发生在体内的折叠过程的逐步反向工程上。
评审人：这篇文章由 Eugene Koonin 和 Frank Eisenhaber 进行了评审。
