Abkevich V I, Gutin A M, Shakhnovich E I
Department of Chemistry, Harvard University, Cambridge Massachusetts 02138.
Biochemistry. 1994 Aug 23;33(33):10026-36. doi: 10.1021/bi00199a029.
We have studied the folding mechanism of lattice model 36-mer proteins. Using a simulated annealing procedure in sequence space, we have designed sequences to have sufficiently low energy in a given target conformation, which plays the role of the native structure in our study. The sequence design algorithm generated sequences for which the native structures is a pronounced global energy minimum. Then, designed sequences were subjected to lattice Monte Carlo simulations of folding. In each run, starting from a random coil conformation, the chain reached its native structure, which is indicative that the model proteins solve the Levinthal paradox. The folding mechanism involved nucleation growth. Formation of a specific nucleus, which is a particular pattern of contacts, is shown to be a necessary and sufficient condition for subsequent rapid folding to the native state. The nucleus represents a transition state of folding to the molten globule conformation. The search for the nucleus is a rate-limiting step of folding and corresponds to overcoming the major free energy barrier. We also observed a folding pathway that is the approach to the native state after nucleus formation; this stage takes about 1% of the simulation time. The nucleus is a spatially localized substructure of the native state having 8 out of 40 native contacts. However, monomers belonging to the nucleus are scattered along the sequence, so that several nucleus contacts are long-range while other are short-range. A folding nucleus was also found in a longer chain 80-mer, where it also constituted 20% of the native structure. The possible mechanism of folding of designed proteins, as well as the experimental implications of this study is discussed.
我们研究了晶格模型36聚体蛋白质的折叠机制。通过在序列空间中使用模拟退火程序，我们设计了在给定目标构象中具有足够低能量的序列，该目标构象在我们的研究中起到天然结构的作用。序列设计算法生成了天然结构为明显全局能量最小值的序列。然后，对设计的序列进行晶格蒙特卡罗折叠模拟。在每次运行中，从无规卷曲构象开始，链达到其天然结构，这表明模型蛋白质解决了莱文塔尔悖论。折叠机制涉及成核生长。形成特定的核，即一种特定的接触模式，被证明是随后快速折叠到天然状态的必要和充分条件。该核代表折叠到熔球构象的过渡态。寻找核是折叠的限速步骤，对应于克服主要的自由能障碍。我们还观察到一种折叠途径，即在核形成后接近天然状态；这个阶段大约占模拟时间的1%。该核是天然状态的空间局部子结构，具有40个天然接触中的8个。然而，属于核的单体沿序列分散，因此一些核接触是长程的，而其他是短程的。在更长的80聚体链中也发现了折叠核，它在那里也构成了天然结构的20%。本文讨论了设计蛋白质可能的折叠机制以及本研究的实验意义。
