β-wrapins are engineered binding proteins stabilizing the β-hairpin conformations of amyloidogenic proteins islet amyloid polypeptide (IAPP), amyloid-β, and α-synuclein, thus inhibiting their amyloid propensity. Here, we use computational and experimental methods to investigate the molecular recognition of IAPP by β-wrapins. We show that the multi-targeted, IAPP, amyloid-β, and α-synuclein, binding properties of β-wrapins originate mainly from optimized interactions between β-wrapin residues and sets of residues in the three amyloidogenic proteins with similar physicochemical properties. Our results suggest that IAPP is a comparatively promiscuous β-wrapin target, probably due to the low number of charged residues in the IAPP β-hairpin motif. The sub-micromolar affinity of β-wrapin HI18, specifically selected against IAPP, is achieved in part by salt-bridge formation between HI18 residue Glu10 and the IAPP N-terminal residue Lys1, both located in the flexible N-termini of the interacting proteins. Our findings provide insights towards developing novel protein-based single- or multi-targeted therapeutics.

β-包裹蛋白是工程化结合蛋白，可稳定淀粉样蛋白生成蛋白胰岛淀粉样多肽 (IAPP)、β-淀粉样蛋白和 α-突触核蛋白的 β-发夹构象，从而抑制其淀粉样蛋白倾向。在这里，我们使用计算和实验方法来研究 β-包裹对 IAPP 的分子识别。我们表明，β-包裹蛋白的多靶点、IAPP、淀粉样蛋白-β和α-突触核蛋白结合特性主要源自β-包裹蛋白残基与具有相似理化特性的三种淀粉样蛋白中的残基组之间的优化相互作用。我们的结果表明，IAPP 是一个相对混杂的 β-wrapin 靶标，可能是由于 IAPP β-发夹基序中带电残基的数量较少。专门针对 IAPP 选择的 β-包裹蛋白 HI18 的亚微摩尔亲和力部分是通过 HI18 残基 Glu10 和 IAPP N 端残基 Lys1 之间形成盐桥来实现的，这两个残基均位于相互作用蛋白的柔性 N 端。我们的研究结果为开发新型基于蛋白质的单靶点或多靶点疗法提供了见解。