从基质绑定PDB结构定义典型蛋白激酶域的活性构造,使所有437个人类催化蛋白激酶的活性状态AlphaFold2模型成为可能
bioRxiv : the preprint server for biology
|February 27, 2026
概括
研究人员定义了活性蛋白激酶的结构标准,发现PDB中只有30%处于活性形式. 他们使用AlphaFold2在活跃状态下建模了所有437个人类激酶,为癌症研究提供了宝贵的资源.
科学领域:
- 结构生物信息学 结构生物信息学
- 计算生物学是一种计算生物学.
- 蛋白激酶的结构动力学结构动力学
背景情况:
- 人类拥有437个具有催化能力的蛋白激酶域,通常采用类似于蛋白激酶A (PKA) 的折叠.
- 激酶的活性构造对于结合ATP,和基质至关重要,但许多在这种状态下没有结构性特征.
- 了解活性激酶结构对于破译基质特异性和突变在癌症等疾病中的影响至关重要.
研究的目的:
- 根据基质结合结构,导出定义蛋白激酶活性形式的结构标准.
- 评估目前在蛋白质数据库 (PDB) 中以活性形式代表的人类蛋白质激酶的比例.
- 使用AlphaFold2.2.生成所有437个人类蛋白激酶在它们的活性构造中的计算模型.
主要方法:
- 对248个基质结合的酶晶体结构进行结构生物信息学分析,以确定活性形式标准.
- 将衍生标准应用于PDB激酶结构,以识别那些具有活性构造的基因结构.
- 利用AlphaFold2,使用PDB模板,序列对齐和活性酶标准,模拟所有437种人类蛋白酶.
主要成果:
- 建立了活性蛋白激酶的结构标准,包括对DFG动机和激活环段的要求.
- 鉴定到,在437种 (30%) 人类催化蛋白激酶中,只有130种在PDB中以其活性形式结构性表现.
- 为所有437个活跃状态的人类蛋白激酶生成了高精度AlphaFold2模型,与PDB结构 (71%<1.0 Å RMSD) 进行了验证.
结论:
- 大多数人体蛋白质激酶在结构数据库中无法以它们的活性形式获得.
- 生成的AlphaFold2模型为了解酶功能,基质特异性和疾病中的突变提供了宝贵的资源.
- 这些模型可以作为模板,用于研究导致癌症构成活性的突变,以及建模基质和抑制剂结合.
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