A structure-based method for derivation of all-atom potentials for protein folding
A structure-based method for derivation of all-atom potentials for protein folding
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DOI：
10.1073/pnas.072665799
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发表时间：
2002-04-16
影响因子：
11.1
通讯作者：
Shakhnovich, EI
中科院分区：
文献类型：
--
作者：
Kussell, E;Shimada, J;Shakhnovich, EI
推导全原子蛋白质折叠潜力的方法，并测试一个三螺旋束蛋白质，以及发夹和螺旋序列。所获得的电位由成对原子之间的接触项和每个原子的局部密度项组成，模仿溶剂暴露偏好。在全原子蛋白质折叠模拟中使用这种势，我们重复折叠三螺旋束，最低能量构象与天然结构的C-alpha距离rms小于2 A。通过使用不同的电势，对于发夹和螺旋获得了类似的结果。我们推导出几种不同蛋白质的电势，并发现推导出的参数之间具有高度相关性，这表明最终可以发现这种形式的电势在原子细节水平上折叠多个不相关的蛋白质。
A method for deriving all-atom protein folding potentials is presented and tested on a three-helix bundle protein, as well as on hairpin and helical sequences. The potentials obtained are composed of a contact term between pairs of atoms, and a local density term for each atom, mimicking solvent exposure preferences. Using this potential in an all-atom protein folding simulation, we repeatedly folded the three-helix bundle, with the lowest energy conformations having a C-alpha distance rms from the native structure of less than 2 A. Similar results were obtained for the hairpin and helices by using different potentials. We derived potentials for several different proteins and found a high correlation between the derived parameters, suggesting that a potential of this form eventually could be found that folds multiple, unrelated proteins at the atomic level of detail.