Daniecki Noah J, Bhatt Megh R, Yap Glenn P A, Zondlo Neal J
Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
Chembiochem. 2022 Dec 16;23(24):e202200409. doi: 10.1002/cbic.202200409. Epub 2022 Nov 24.
Proline residues within proteins lack a traditional hydrogen bond donor. However, the hydrogens of the proline ring are all sterically accessible, with polarized C-H bonds at Hα and Hδ that exhibit greater partial positive character and can be utilized as alternative sites for molecular recognition. C-H/O interactions, between proline C-H bonds and oxygen lone pairs, have been previously identified as modes of recognition within protein structures and for higher-order assembly of protein structures. In order to better understand intermolecular recognition of proline residues, a series of proline derivatives was synthesized, including 4R-hydroxyproline nitrobenzoate methyl ester, acylated on the proline nitrogen with bromoacetyl and glycolyl groups, and Boc-4S-(4-iodophenyl)hydroxyproline methyl amide. All three derivatives exhibited multiple close intermolecular C-H/O interactions in the crystallographic state, with H⋅⋅⋅O distances as close as 2.3 Å. These observed distances are well below the 2.72 Å sum of the van der Waals radii of H and O, and suggest that these interactions are particularly favorable. In order to generalize these results, we further analyzed the role of C-H/O interactions in all previously crystallized derivatives of these amino acids, and found that all 26 structures exhibited close intermolecular C-H/O interactions. Finally, we analyzed all proline residues in the Cambridge Structural Database of small-molecule crystal structures. We found that the majority of these structures exhibited intermolecular C-H/O interactions at proline C-H bonds, suggesting that C-H/O interactions are an inherent and important mode for recognition of and higher-order assembly at proline residues. Due to steric accessibility and multiple polarized C-H bonds, proline residues are uniquely positioned as sites for binding and recognition via C-H/O interactions.
蛋白质中的脯氨酸残基缺乏传统的氢键供体。然而，脯氨酸环上的氢在空间上都是可接近的，Hα和Hδ处的C-H键具有极化性，表现出更大的部分正电荷特性，可作为分子识别的替代位点。脯氨酸C-H键与氧孤对之间的C-H/O相互作用，先前已被确定为蛋白质结构内的识别模式以及蛋白质结构高阶组装的模式。为了更好地理解脯氨酸残基的分子间识别，合成了一系列脯氨酸衍生物，包括4R-羟基脯氨酸硝基苯甲酸甲酯、在脯氨酸氮上用溴乙酰基和乙醇酰基酰化的产物，以及Boc-4S-(4-碘苯基)羟基脯氨酸甲酰胺。所有这三种衍生物在晶体状态下都表现出多个紧密的分子间C-H/O相互作用，H⋅⋅⋅O距离近至2.3 Å。这些观察到的距离远低于H和O范德华半径之和2.72 Å，表明这些相互作用特别有利。为了推广这些结果，我们进一步分析了C-H/O相互作用在这些氨基酸所有先前结晶衍生物中的作用，发现所有26个结构都表现出紧密的分子间C-H/O相互作用。最后，我们分析了小分子晶体结构剑桥结构数据库中的所有脯氨酸残基。我们发现这些结构中的大多数在脯氨酸C-H键处表现出分子间C-H/O相互作用，这表明C-H/O相互作用是脯氨酸残基识别和高阶组装的固有且重要的模式。由于空间可及性和多个极化的C-H键，脯氨酸残基通过C-H/O相互作用作为结合和识别位点具有独特的地位。
