Statistical mechanics of helix bundles using a dynamic programming approach.
Statistical mechanics of helix bundles using a dynamic programming approach.
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使用动态规划方法的螺旋束统计力学。
DOI：
10.1021/ja067153s
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发表时间：
2007
影响因子：
15
通讯作者：
Dill,KenA
中科院分区：
文献类型：
--
作者：
Lucas,Adam;Huang,Liang;Joshi,Aravind;Dill,KenA
尽管进行了大量研究，但生物分子折叠协同性仍不清楚。有螺旋-螺旋转变和螺旋-球状转变的定量模型，但还没有准确的模型同时处理链塌陷和二级结构形成。我们在这里开发了一种动态规划方法来计算文件夹链分子的统计机械配分函数。我们称之为上升水平模型。我们将其应用于螺旋线圈和螺旋束折叠和协同性。对于 14 至 50 聚体 Baldwin 肽，该模型可以很好地预测热容量和螺旋度与温度和尿素的关系。该模型还很好地拟合了 Oas 蛋白 A (F13W*) 的三螺旋束 B 结构域和合成蛋白 α3C 在温度和胍作用下的变性。该模型预测构象分布。它表明这些蛋白质以两种状态的转变折叠，尽管鲍德温螺旋中的转变几乎是更高阶的。该模型显示 Lee 等人最近开发的三螺旋束多肽。反合作折叠，预测值为 ΔHvH/ΔHcal= 0.72。该模型还预测双螺旋束在蛋白质中不稳定，但在类肽中稳定。我们的动态编程方法提供了一种探索复杂可折叠聚合物中协同性的通用方法。
Despite much study, biomolecule folding cooperativity is not well understood. There are quantitative models for helix-coil transitions and for coil-to-globule transitions, but no accurate models yet treat both chain collapse and secondary structure formation together. We develop here a dynamic programming approach to statistical mechanical partition functions of foldamer chain molecules. We call it the ascending levels model. We apply it to helix-coil and helix-bundle folding and cooperativity. For 14- to 50-mer Baldwin peptides, the model gives good predictions for the heat capacity and helicity versus temperature and urea. The model also gives good fits for the denaturation of Oas's three-helix bundle B domain of protein A (F13W*) and synthetic protein α3Cby temperature and guanidine. The model predicts the conformational distributions. It shows that these proteins fold with transitions that are two-state, although the transitions in the Baldwin helices are nearly higher order. The model shows that the recently developed three-helix bundle polypeptoids of Lee et al. foldanti-cooperatively, with a predicted value of ΔHvH/ΔHcal= 0.72. The model also predicts that two-helix bundles are unstable in proteins but stable in peptoids. Our dynamic programming approach provides a general way to explore cooperativity in complex foldable polymers.