Conformational analysis of peptide surrogates. Reduced and retro-amide links in blocked alanine and in secondary structures.

P Dauber-Osguthorpe, M M Campbell, D J Osguthorpe
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Abstract

We have investigated the conformational effects of modifying the amide link of peptides. We studied a reverse amide bond psi [NHCO], a reduced amide bond psi [CH2NH] and a retro-reduced bond psi [NHCH2] as surrogates for the amide link [CONH] in native peptides. A complete search of the conformational space available to residues with these modified links was carried out. The local minima and the rotational barriers were described and compared to the minima of the native residue. The results are compatible with the available observed structural data. These modified links have been incorporated in secondary structure units such as beta turns, alpha helices, and parallel and anti-parallel beta sheets. It was found that a reduced amide link can lead to stabilised beta turns, while the retro modification can be incorporated in stable beta sheets. A significant reduction in the stability of alpha helices is caused by the retro links, while a reduced amide link results in only a small destabilisation.

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肽替代物的构象分析。阻断丙氨酸和二级结构中的减少和反酰胺连接。
我们研究了修饰肽的酰胺键对构象的影响。我们研究了一个反酰胺键psi [NHCO],一个还原酰胺键psi [CH2NH]和一个还原酰胺键psi [NHCH2]作为天然肽中酰胺键[CONH]的替代品。对具有这些修饰链的残基的构象空间进行了完整的搜索。描述了局部极小值和旋转势垒,并与自然残差的极小值进行了比较。计算结果与现有的结构观测数据一致。这些改进的连杆已被纳入二级结构单元,如β匝、α螺旋、平行和反平行β片。研究发现,减少酰胺连接可以导致稳定的β转,而复古修饰可以纳入稳定的β片。α螺旋稳定性的显著降低是由复古连接引起的,而酰胺连接的减少只会导致小的不稳定性。
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