含Asn-Gly的七肽形成$β$ -转角结构的倾向性：量子力学从头计算与分子动力学模拟的比较
On the propensity of Asn-Gly-containing heptapeptides to form $β$-turn structures : comparison between ab initio quantum mechanical calculations and Molecular Dynamics simulations
摘要：
分子力学和量子力学计算在描述分子的行为和结构中起着重要的作用。在这项工作中，我们比较了相同的肽系统的折叠分子动力学模拟与以前报道的结果从量子力学计算得到的结果。更具体地说，为了研究它们的折叠和动力学，对三种含Asn-Gly的七肽进行了各自在显式水溶剂中的5个$μ$的三个分子动力学模拟。基于量子力学计算和DFT方法的先前数据已经表明，这些肽在水溶液中采用$β$ -转角结构，其中I'型$β$ -转角是最优选的基序。从我们的分析结果表明，对于给定的系统，这两种方法在他们的预测分歧。力场依赖的缺陷的可能性被检查作为所观察到的差异的可能来源。
英文摘要：
Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 $μ$s each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations and the DFT methods have shown that these peptides adopt $β$-turn structures in aqueous solution, with type I' $β$-turn being the most preferred motif. The results from our analyses indicate that for the given system the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.
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