School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
Biochem Biophys Res Commun. 2019 Sep 3;516(4):1123-1129. doi: 10.1016/j.bbrc.2019.07.006. Epub 2019 Jul 5.
Methionine aminopeptidase 2 (MetAP2) is one of the effector proteins of S100A4, a metastasis-associated calcium-binding protein. This interaction is involved in angiogenesis. The region of MetAP2 that interacts with S100A4 includes amino acids 170 to 208. A peptide corresponding to this region, named as NBD, has potent anti-angiogenic activity and suppresses tumor growth in a xenograft cancer model. However, the binding mode of NBD to S100A4 was totally unknown. Here we describe our analysis of the relationship between the inhibitory activity and the structure of NBD, which adopts a characteristic helix-turn-helix structure as shown by X-ray crystallographic analysis, and peptide fragments of NBD. We conducted physicochemical analyses of the interaction between S100A4 and the peptides, including surface plasmon resonance, microscale thermophoresis, and circular dichroism, and performed docking/molecular dynamics simulations. Active peptides had stable secondary structures, whereas inactive peptides had a little secondary structure. A computational analysis of the interaction mechanism led to the design of a peptide smaller than NBD, NBD-ΔN10, that possessed inhibitory activity. Our study provides a strategy for design for a specific peptide inhibitor against S100A4 that can be applied to the discovery of inhibitors of other protein-protein interactions.
甲硫氨酸氨肽酶 2（MetAP2）是 S100A4（一种与转移相关的钙结合蛋白）的效应蛋白之一。这种相互作用涉及血管生成。与 S100A4 相互作用的 MetAP2 区域包括氨基酸 170 到 208。与该区域相对应的肽，称为 NBD，具有很强的抗血管生成活性，并在异种移植癌症模型中抑制肿瘤生长。然而，NBD 与 S100A4 的结合模式完全未知。在这里，我们描述了我们对 NBD 的抑制活性与结构之间关系的分析，该结构通过 X 射线晶体学分析显示出特征性的螺旋-转角-螺旋结构，以及 NBD 的肽片段。我们对 S100A4 与肽之间的相互作用进行了物理化学分析，包括表面等离子体共振、微量热泳动和圆二色性，并进行了对接/分子动力学模拟。活性肽具有稳定的二级结构，而无活性肽的二级结构很少。对相互作用机制的计算分析导致了设计出一种比 NBD 更小的肽，NBD-ΔN10，具有抑制活性。我们的研究为设计针对 S100A4 的特异性肽抑制剂提供了一种策略，可应用于其他蛋白质-蛋白质相互作用抑制剂的发现。
