Glycine in Water Favors the Polyproline II State
Glycine in Water Favors the Polyproline II State
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DOI：
10.3390/biom10081121
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发表时间：
2020-08-01
期刊：
影响因子：
5.5
通讯作者：
Urbanc, Brigita
中科院分区：
文献类型：
--
作者：
Andrews, Brian;Zhang, Shuting;Urbanc, Brigita
氨基酸残基在水中的构象偏好由主链和侧链性质决定。丙氨酸以其高聚脯氨酸II（pPII）倾向而闻名。主链和侧链对丙氨酸和其他氨基酸残基在水中的构象偏好的相对贡献的问题尚未完全解决。由于甘氨酸缺乏重原子侧链，基于甘氨酸的肽可用于检查主链性质影响构象空间的程度。在这里，我们使用已发表的光谱数据的阳离子三甘氨酸在水中的中心甘氨酸残基，以证明其构象空间是由pPII状态为主。我们评估三种常用的分子动力学（MD）力场就其捕获的能力，在三甘氨酸的中心甘氨酸残基的构象偏好。我们表明，pPII是介观状态，使中心残基的功能性骨干基团，以形成最氢键与水。我们的研究结果表明，GGG中的中心甘氨酸的pPII倾向与GAG中的丙氨酸的pPII倾向相当，这意味着水-骨架氢键是负责这些残基的高pPII含量。
Conformational preferences of amino acid residues in water are determined by the backbone and side-chain properties. Alanine is known for its high polyproline II (pPII) propensity. The question of relative contributions of the backbone and side chain to the conformational preferences of alanine and other amino acid residues in water is not fully resolved. Because glycine lacks a heavy-atom side chain, glycine-based peptides can be used to examine to which extent the backbone properties affect the conformational space. Here, we use published spectroscopic data for the central glycine residue of cationic triglycine in water to demonstrate that its conformational space is dominated by the pPII state. We assess three commonly used molecular dynamics (MD) force fields with respect to their ability to capture the conformational preferences of the central glycine residue in triglycine. We show that pPII is the mesostate that enables the functional backbone groups of the central residue to form the most hydrogen bonds with water. Our results indicate that the pPII propensity of the central glycine in GGG is comparable to that of alanine in GAG, implying that the water-backbone hydrogen bonding is responsible for the high pPII content of these residues.