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.

中文翻译：

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水中的甘氨酸有利于Polyproline II态。

水中氨基酸残基的构象偏好由主链和侧链特性决定。丙氨酸因其高脯氨酸II（pPII）倾向而闻名。骨架和侧链对水中丙氨酸和其他氨基酸残基构象偏好的相对贡献问题尚未完全解决。由于甘氨酸缺少重原子侧链，因此可以使用基于甘氨酸的肽来检查骨架性质在多大程度上影响构象空间。在这里，我们使用公开的光谱数据来分析水中阳离子三甘氨酸的中央甘氨酸残基，以证明其构象空间由pPII状态决定。我们评估了三个常用的分子动力学（MD）力场，以捕获三甘氨酸中中央甘氨酸残基的构象偏好。我们表明，pPII是使中间残基的功能性主链基团与水形成最多氢键的中间态。我们的结果表明，GGG中的中央甘氨酸的pPII倾向与GAG中的丙氨酸相当，这表明水-骨干氢键是这些残基中pPII含量高的原因。