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图表注意力神经网络揭示了CRISPR相关的转子子子中的TnsC线程组合

Chinmai Pindi¹, Mohd Ahsan¹, Souvik Sinha¹

¹Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States.

bioRxiv : the preprint server for biology

|July 16, 2025

概括

与CRISPR相关的转体子 (CAST) 使用TnsC蛋白来整合DNA. 这项研究揭示了TnsC如何在DNA上形成丝,受ATP结合和特定蛋白质-DNA相互作用的引导,从而实现精确的基因组工程.

科学领域:

分子生物学分子生物学
基因组学就是基因组学.
生物物理学的生物物理.

背景情况:

与CRISPR相关的转子子 (CAST) 是可编程DNA集成在基因组工程中的强大工具.
AAA+ ATPase TnsC对于类型V-K CAST系统至关重要,在双链DNA (dsDNA) 上形成螺旋丝,以直接转换.
对于TnsC光纤核和延长的精确机制还没有完全理解.

研究的目的:

阐明调控TnsC线丝形成和生长的分子机制.
研究ATP结合和蛋白质-DNA相互作用在TnsC核形成中的作用.
了解TnsC线丝延长沿着dsDNA的方向动力学.

主要方法:

利用多个微秒的分子动力学模拟.
使用自由能量模拟来分析蛋白质-DNA相互作用.
开发并应用基于深度学习的图形注意力网络 (GAT) 模型.

主要成果:

发现ATP结合通过诱导DNA重塑和稳定关键蛋白质-DNA相互作用,特别是通过启动器特异性动机 (ISM) 来促进TnsC核形成.
图形神经网络 (GNN) 分析显示了丝长度的方向偏差 (5'→3').
确定了传入和结合单体之间的动态补偿机制,促进了定向增长.

结论:

在V-K型CAST系统中建立了TnsC光纤动态和定向延长的机制框架.
证明了基于深度学习的GAT模型对解释复杂分子模拟的实用性.
为更精确,更有效的基因组工程CAST系统的合理设计提供了见解.

关键词:

AAA+AAA+是什么意思这就是CRISPR-Cas.人工智能的人工智能是人工智能.基因组编辑基因组编辑神经网络的神经网络的神经网络

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