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首页> 外文期刊>Journal of Molecular Biochemistry >Prediction of Peptide Binding to Major Histocompatibility II Receptors with Molecular Mechanics and Semi-Empirical Quantum Mechanics Methods
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Prediction of Peptide Binding to Major Histocompatibility II Receptors with Molecular Mechanics and Semi-Empirical Quantum Mechanics Methods

机译：用分子力学和半经验量子力学方法预测与主要组织相容性II受体结合的肽

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Methods for prediction of the binding of peptides to major histocompatibility complex (MHC) II receptors are examined, using literature values of IC50 as a benchmark. Two sets of IC50 data for closely structurally related peptides based on hen egg lysozyme (HEL) and myelin basic protein (MBP) are reported first. This shows that methods based on both molecular mechanics and semi-empirical quantum mechanics can predict binding with good-to-reasonable accuracy, as long as a suitable method for estimation of solvation effects is included. A more diverse set of 22 peptides bound to HLA-DR1 provides a tougher test of such methods, especially since no crystal structure is available for these peptide-MHC complexes. We therefore use sequence based methods such as SYFPEITHI and SVMHC to generate possible binding poses, using a consensus approach to determine the most likely anchor residues, which are then mapped onto the crystal structure of an unrelated peptide bound to the same receptor. This analysis shows that the MM/GBVI method performs particularly well, as does the AMBER94 forcefield with Born solvation model. Indeed, MM/GBVI can be used as an alternative to sequence based methods in generating binding poses, leading to still better accuracy.
机译：使用IC50的文献资料作为基准，检验了预测肽与主要组织相容性复合物（MHC）II受体结合的方法。首先报道了两组基于鸡蛋溶菌酶（HEL）和髓磷脂碱性蛋白（MBP）的紧密结构相关肽的IC50数据。这表明，基于分子力学和半经验量子力学的方法都可以预测结合，只要达到估计溶剂化效果的合适方法即可。与HLA-DR1结合的22种肽的多样性更为多样化，对此类方法进行了更严格的测试，尤其是因为这些肽-MHC复合物没有晶体结构可用。因此，我们使用基于序列的方法（例如SYFPEITHI和SVMHC）来生成可能的结合姿势，并使用共有方法确定最可能的锚残基，然后将其定位到与相同受体结合的无关肽的晶体结构上。该分析表明，MM / GBVI方法的性能特别好，带有Born溶剂化模型的AMBER94力场也是如此。实际上，MM / GBVI可以用作生成绑定姿势的基于序列的方法的替代方法，从而带来更高的准确性。

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