Three-body interactions improve the prediction of rate and mechanism in protein folding models
Three-body interactions improve the prediction of rate and mechanism in protein folding models
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DOI：
10.1073/pnas.0403486101
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发表时间：
2004-10-19
影响因子：
11.1
通讯作者：
Plotkin, SS
中科院分区：
文献类型：
--
作者：
Ejtehadi, MR;Avall, SP;Plotkin, SS
在这里，我们利用大量粗粒C-α模型单域蛋白质的分子动力学模拟结果，研究了多体相互作用对蛋白质折叠速度和机制的影响。在将三体相互作用明确地作为扰动添加到仅具有自然成对相互作用的GO类哈密顿量后，我们发现：(I)与实验的phi值和折叠速度的相关性显著增加，(Ii)折叠速度与接触顺序的相关性更强，当自然状态的三体能量的比例约为20%时，折叠速度与实验范围相符，以及(Iii)凝乳酶抑制剂中存在的三体能量比其他所研究的蛋白质中的三体能量要大得多。
Here we study the effects of many-body interactions on rate and mechanism in protein folding by using the results of molecular dynamics simulations on numerous coarse-grained C-alpha-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Go-like Hamiltonian with native pairwise interactions only, we have found (i) a significantly increased correlation with experimental phi values and folding rates, (ii) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is approximate to20%, and (iii) a considerably larger amount of three-body energy present in chymotripsin inhibitor than in the other proteins studied.