School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China.
Phys Chem Chem Phys. 2022 May 25;24(20):12267-12280. doi: 10.1039/d2cp00569g.
Amyloid precursor protein (APP) is the core of the pathogenesis of Alzheimer's disease (AD). Existing studies have shown that the soluble secreted APP (sAPPα) fragment obtained from the hydrolysis of APP by α-secretase has a synaptic function. Thereinto, a nine-residue fragment (APP9mer) of the extension domain region of sAPPα can bind directly and selectively to the N-terminal sushi1 domain (SD1) of the γ-aminobutyric acid type B receptor subunit 1a (GABAR1a) protein, which can influence synaptic transmission and plasticity by changing the GABAR1a conformation. APP9mer is a highly flexible, disordered region, and as such it is difficult to experimentally determine the optimal APPmer-SD1 binding complex. In this study we constructed two types of APP9mer-SD1 complexes through molecular docking and molecular dynamics simulation, aiming to explore the recognition function and mechanism of the specific binding of APP9mer with SD1, from which the most probable APPmer-SD1 model conformation is predicted. All the data from the analyses of RMSD, RMSF, PCA, DCCM and MM/PBSA binding energy as well as comparison with the experimental dissociation constant suggest that 2NC is the most likely conformation to restore the crystal structure of the experimental APP9mer-SD1 complex. Of note, the key recognition residues of APP9mer are D24, D25, D27, W29 and W30, which mainly act on the 9-45 residue domain of SD1 (consisting of two loops and three short β-chains at the N-terminus of SD1). The mini-model with key residues identified establishes the molecular basis with deep insight into the interaction between APP and GABAR1a and provides a target for the development of therapeutic strategies for modulating GABAR1a-specific signaling in neurological and psychiatric disorders. More importantly, the study offers a theoretical solution for how to determine a biomolecular structure with a highly flexible, disordered fragment embedded within. The flexible fragment involved in a protein structure has to be deserted usually during the structural determination with experimental methods ( X-ray crystallography, ).
淀粉样前体蛋白（APP）是阿尔茨海默病（AD）发病机制的核心。现有研究表明，APP 经 α-分泌酶水解得到的可溶分泌型 APP（sAPPα）片段具有突触功能。其中，sAPPα延伸结构域的一个九肽片段（APP9mer）可直接和选择性地与 γ-氨基丁酸 B 型受体亚基 1a（GABAR1a）蛋白的 N 端 sushi1 结构域（SD1）结合，通过改变 GABAR1a 构象影响突触传递和可塑性。APP9mer 是一个高度灵活的无规卷曲区域，因此难以通过实验确定 APP9mer-SD1 最佳结合复合物。本研究通过分子对接和分子动力学模拟构建了两种 APP9mer-SD1 复合物，旨在探索 APP9mer 与 SD1 特异性结合的识别功能和机制，预测最可能的 APP9mer-SD1 模型构象。通过分析 RMSD、RMSF、PCA、DCCM 和 MM/PBSA 结合能以及与实验解离常数的比较，得出所有数据均表明 2NC 是最有可能恢复实验 APP9mer-SD1 复合物晶体结构的构象。值得注意的是，APP9mer 的关键识别残基为 D24、D25、D27、W29 和 W30，主要作用于 SD1 的 9-45 位残基域（由 SD1 氨基端的两个环和三个短β-链组成）。确定关键残基的迷你模型建立了深入了解 APP 与 GABAR1a 相互作用的分子基础，并为调节神经和精神疾病中 GABAR1a 特异性信号的治疗策略开发提供了靶点。更重要的是，该研究为如何确定包含高度灵活的无序片段的生物分子结构提供了理论解决方案。通常在使用实验方法（X 射线晶体学）进行结构测定时，需要舍弃蛋白质结构中涉及的柔性片段。
