Ramírez-Alvarado M, Blanco F J, Niemann H, Serrano L
European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany.
J Mol Biol. 1997 Nov 7;273(4):898-912. doi: 10.1006/jmbi.1997.1347.
The sequence RGITVNGKTYGR has been reported as part of a de novo design peptide system. This peptide folds as a beta-hairpin structure with three residues per strand and two residue turns. Asn6 side-chain, the residue in position L1 of the beta-turn, appeared to be solvent exposed, interacting only within the turn but not with the rest of the peptide. We have chosen this position as a good candidate to design mutations, based on the protein database statistical abundances, that should mainly affect the turn stability and possibly the pairing between strands. We have found that all NMR parameters, in particular the conformational shift analysis of CalphaH and the coupling constants, 3JHNalpha, correlate very well and show similar conformational features in all the turn mutant peptides. The population estimates are in reasonable agreement among the different methods used. It appears that the peptide with Asn in position L1 is the most structured peptide, followed by the one with Asp6. The next structured peptide is the one with Gly6. The least populated peptides were those with Ala6 and Ser6. We have found a strong correlation between the hairpin population, as determined from the conformational shift of CalphaH and the occurrence of the different residues at position L1 of beta-hairpins with type I' beta-turn, in the protein database. Our analysis demonstrates that this peptide system is sensitive enough to register small energy changes in the hairpin structure; therefore, it constitutes an appropriate model to quantify energy contributions, once the appropriate sheet/coil transition algorithm is developed. Comparison with the other studies indicate that the design of a specific hairpin structure must involve a sequence at the turn region favouring the desired turn type, and a sequence at the strands that avoids alternative interstrand side-chain pairings.
序列RGITVNGKTYGR已被报道为一种从头设计肽系统的一部分。该肽折叠成β-发夹结构，每条链有三个残基，转角处有两个残基。Asn6侧链，即β-转角L1位置的残基，似乎暴露于溶剂中，仅在转角内相互作用，而不与肽的其余部分相互作用。基于蛋白质数据库的统计丰度，我们选择这个位置作为设计突变的良好候选位点，这些突变应该主要影响转角稳定性，并可能影响链间配对。我们发现，所有核磁共振参数，特别是CαH的构象位移分析和耦合常数3JHNα，都具有很好的相关性，并且在所有转角突变肽中都显示出相似的构象特征。在使用的不同方法中，种群估计结果相当一致。似乎L1位置为Asn的肽是结构最稳定的肽，其次是Asp6的肽。下一个结构稳定的肽是Gly6的肽。种群数量最少的肽是Ala6和Ser6的肽。我们发现，根据CαH的构象位移确定的发夹种群与蛋白质数据库中具有I'型β-转角的β-发夹L1位置不同残基的出现之间存在很强的相关性。我们的分析表明，这个肽系统足够敏感，能够记录发夹结构中的微小能量变化；因此，一旦开发出合适的片层/卷曲转变算法，它就构成了一个量化能量贡献的合适模型。与其他研究的比较表明，特定发夹结构的设计必须在转角区域包含有利于所需转角类型的序列，以及在链上包含避免链间侧链配对的序列。
