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Generalized Born Implicit Solvent Models Do Not Reproduce Secondary Structures of De Novo Designed Glu/Lys Peptides
Journal of Chemical Theory and Computation ( IF 5.7 ) Pub Date : 2022-06-10 , DOI: 10.1021/acs.jctc.1c01172
Eric J M Lang 1, 2, 3 , Emily G Baker 2, 3 , Derek N Woolfson 2, 3, 4 , Adrian J Mulholland 1, 2
Affiliation  

We test a range of standard generalized Born (GB) models and protein force fields for a set of five experimentally characterized, designed peptides comprising alternating blocks of glutamate and lysine, which have been shown to differ significantly in α-helical content. Sixty-five combinations of force fields and GB models are evaluated in >800 μs of molecular dynamics simulations. GB models generally do not reproduce the experimentally observed α-helical content, and none perform well for all five peptides. These results illustrate that these models are not usefully predictive in this context. These peptides provide a useful test set for simulation methods.

中文翻译:

广义 Born 隐式溶剂模型不会重现从头设计的 Glu/Lys 肽的二级结构

我们测试了一系列标准广义 Born (GB) 模型和蛋白质力场,用于一组五种经过实验表征的设计肽,包括交替的谷氨酸和赖氨酸块,这些肽已被证明在 α-螺旋含量上有显着差异。在 >800 μs 的分子动力学模拟中评估了力场和 GB 模型的 65 种组合。GB 模型通常不会重现实验观察到的 α-螺旋含量,并且所有五种肽都没有表现良好。这些结果表明,这些模型在这种情况下没有有用的预测性。这些肽为模拟方法提供了有用的测试集。
更新日期:2022-06-10
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