Energetic contribution to both acidity and conformational stability in peptide models
Energetic contribution to both acidity and conformational stability in peptide models
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DOI：
10.1039/c5nj03611a
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发表时间：
2016-06-01
影响因子：
3.3
通讯作者：
Budisa, Nediljko
中科院分区：
文献类型：
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作者：
Kubyshkin, Vladimir;Durkin, Patrick;Budisa, Nediljko
n -酰基氨基酸的酸度取决于酰胺键的旋美态。在这项工作中，我们系统地研究了各种乙酰化氨基酸框架中旋转体（δ pK(a)）的酸度差异。我们的结果表明两个具有吸引力的羰基相互作用。对于无环氨基酸，我们观察到保守的δ pK(a)s (2.2-3.0 kJ mol(-1))，而对于脂环氨基酸，实验值显示强烈依赖于结构背景（1.5-4.4 kJ mol(-1)）。在同源氨基酸（α -, β -， γ -等）中，吸引力的强度以指数方式衰减。此外，这种相互作用可以通过酰胺键链以级联方式积累，如Ac-Pro-Pro二肽所示。因此，我们证明了Delta pK(a)是一个实验参数，用于估计羰基-羰基排列的增量，由氨基酸或肽基环境决定。这个参数对于理解氨基酸在生物系统中蛋白质折叠和翻译中的作用以及它们在遗传密码中的进化外观也很重要。
The acidity of N-acyl amino acids is dependent upon the rotameric state of the amide bond. In this work we systematically investigated the acidity difference of the rotamers (Delta pK(a)) in the frames of various acetylated amino acids. Our results indicated a mutual interaction of two carbonyl groups of an attractive type. We observed conservative Delta pK(a)s for acyclic amino acids (2.2-3.0 kJ mol(-1)), whereas in the case of alicyclic amino acids, the experimental values revealed a strong dependency on the structural context (1.5-4.4 kJ mol(-1)). In homologous amino acids (alpha-, beta-, gamma-, etc.), the strength of the attraction decays in an exponential fashion. Furthermore, the interaction can accumulate through a chain of amide bonds in a cascade fashion, as demonstrated by an Ac-Pro-Pro dipeptide. As a result, we demonstrate that Delta pK(a) is an experimental parameter to estimate increments in the carbonyl-carbonyl alignment, as determined by the amino acid or peptidyl context. This parameter is also important in understanding the roles of amino acids in both protein folding and translation in biological systems as well as their evolutionary appearance in the genetic code.