The functional capacity of the natural amino acids for molecular recognition
The functional capacity of the natural amino acids for molecular recognition
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DOI：
10.1039/b927393j
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发表时间：
2010-01-01
影响因子：
--
通讯作者：
Sidhu, Sachdev S.
中科院分区：
文献类型：
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作者：
Birtalan, Sara;Fisher, Robert D.;Sidhu, Sachdev S.
我们在二元Tyr/Ser多样性的最小背景下测试了天然氨基酸对分子识别的功能能力。在噬菌体展示的合成抗体库中，我们用其他残基替换了Tyr或Ser。我们发现，对于既有利于亲和力又有利于特异性的联系，Tyr是最佳的中介联系，但它可以被Trp取代，这有利于亲和力但不利于特异性。Arg在介导分子识别方面的能力有限，但不如Tyr或Trp有效，而且是非特异性相互作用的主要贡献者。其他9种残留类型(Phe、Leu、Ile、Asn、Thr、Pro、Cys、Ala和Gly)被发现不能作为Tyr的替代品。通过用Gly或Ala取代Ser，我们发现Gly和Ser一样有效地提供构象灵活性，使笨重的Tyr残基实现最佳结合接触，而Ala则不那么有效，但仍具有这种功能。对于一些抗原，仅使用Tyr/Ser/Gly多样性就可以获得高亲和力抗体，但对于其他抗原，需要额外的化学多样性才能获得高亲和力。我们的结果为合成抗原结合位点建立了一个最小的基准，其亲和力与天然抗体相当。此外，我们的发现阐明了蛋白质-蛋白质相互作用的基本原理，并为设计功能超出天然蛋白质范围的合成结合蛋白质提供了有价值的指导方针。
We tested the functional capacity of the natural amino acids for molecular recognition in a minimalist background of binary Tyr/Ser diversity. In phage-displayed synthetic antibody libraries, we replaced either Tyr or Ser with other residues. We find that Tyr is optimal for mediating contacts that contribute favourably to both affinity and specificity, but it can be replaced by Trp, which contributes favourably to affinity but is detrimental to specificity. Arg exhibited a limited capacity for mediating molecular recognition but was less effective than either Tyr or Trp, and moreover, was the major contributor to non-specific interactions. Nine other residue types (Phe, Leu, Ile, Asn, Thr, Pro, Cys, Ala, and Gly) were found to be ineffective as replacements for Tyr. By replacing Ser with Gly or Ala, we found that Gly is as effective as Ser for providing conformational flexibility that allows bulky Tyr residues to achieve optimal binding contacts, while Ala is less effective but still functional in this capacity. For some antigens, high affinity antibodies could be derived using only Tyr/Ser/Gly diversity, but for others, additional chemical diversity was required to achieve high affinity. Our results establish a minimal benchmark for the generation of synthetic antigen-binding sites with affinities comparable to those of natural antibodies. Moreover, our findings illuminate the fundamental principles underlying protein-protein interactions and provide valuable guidelines for engineering synthetic binding proteins with functions beyond the scope of natural proteins.