PROTEIN CORE ASSEMBLY PROCESSES
PROTEIN CORE ASSEMBLY PROCESSES
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DOI：
10.1063/1.464068
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发表时间：
1993-02-15
影响因子：
4.4
通讯作者：
DILL, KA
中科院分区：
文献类型：
--
作者：
FIEBIG, KM;DILL, KA
蛋白质或HP（疏水/极性）共聚物如何在没有全局穷举搜索的情况下找到其全局最优（天然）状态？这就是莱文塔尔悖论。我们考虑了三种使共聚物可以组装成具有最大数量疏水（HH）接触的紧凑构象的途径：（i）确保全局最优的穷举搜索（ES）过程;（ii）“最大熵串”（MES），一系列逐步决策，每个决策对给定的先前接触穷举地探索构象空间;以及（iii）“T-局部串”或“疏水拉链”（HZ）过程，其基于先前接触机会性地产生HH接触。使用二维HP短链格点模型，其中的配分函数是精确的，我们发现，对于许多HP序列，T-本地字符串导致的全局最优构象，提供了解决Levinthal悖论。
How does a protein or HP (hydrophobic/polar) copolymer find its globally optimal (native) state without a globally exhaustive search? This is the Levinthal paradox. We consider three routes by which a copolymer might assemble a compact conformation with a maximum number of hydrophobic (HH) contacts: (i) the exhaustive search (ES) process, which assures the global optimum; (ii) a ''maximum entropy string'' (MES), a series of stepwise decisions each of which explores conformational space exhaustively for given prior contacts; and (iii) a ''T-local string,'' or ''hydrophobic zippers'' (HZ) process, which makes HH contacts opportunistically based on prior contacts. Using a two-dimensional HP short-chain lattice model, for which the partition function is exactly enumerable, we find that for many HP sequences, T-local strings lead to the globally optimal conformation, offering a resolution to the Levinthal paradox.