Department of Chemistry, Korea University, Seoul 136-701, Korea.
Proteins. 2012 Apr;80(4):977-90. doi: 10.1002/prot.24000. Epub 2012 Jan 4.
Despite prolonged scientific efforts to elucidate the intrinsic peptide backbone preferences of amino-acids based on understanding of intermolecular forces, many open questions remain, particularly concerning neighboring peptide interaction effects on the backbone conformational distribution of short peptides and unfolded proteins. Here, we show that spectroscopic studies of a complete library of 400 dipeptides reveal that, irrespective of side-chain properties, the backbone conformation distribution is narrow and they adopt polyproline II and β-strand, indicating the importance of backbone peptide solvation and electronic effects. By directly comparing the dipeptide circular dichroism and NMR results with those of unfolded proteins, the comprehensive dipeptides form a complete set of structural motifs of unfolded proteins. We thus anticipate that the present dipeptide library with spectroscopic data can serve as a useful database for understanding the nature of unfolded protein structures and for further refinements of molecular mechanical parameters.
尽管科学界为了阐明基于对分子间力理解的氨基酸的内在肽骨架偏好性进行了长期努力，但仍有许多悬而未决的问题，特别是关于短肽和未折叠蛋白质的相邻肽相互作用对骨架构象分布的影响。在这里，我们展示了对包含 400 种二肽的完整文库的光谱研究表明，无论侧链性质如何，骨架构象分布都很狭窄，它们采用多脯氨酸 II 和 β-折叠，这表明了肽溶剂化和电子效应的重要性。通过将二肽圆二色性和 NMR 结果与未折叠蛋白质的结果直接进行比较，全面的二肽形成了未折叠蛋白质结构的完整基序集。因此，我们预计本带有光谱数据的二肽文库可以作为理解未折叠蛋白质结构的本质和进一步改进分子力学参数的有用数据库。
