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准确模拟蛋白质二次结构和相位分离之间的合

Yumeng Zhang¹, Shanlong Li¹, Xiping Gong¹

¹Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States.

Journal of the American Chemical Society

|December 19, 2023

概括

一个新的混合分辨率 (HyRes) 蛋白模型准确地模拟了内在无序的蛋白质 (IDP) 阶段分离,捕捉了对生物分子凝聚物形成至关重要的骨干和次要结构效应.

科学领域:

生物物理
计算生物学
蛋白质科学

背景情况:

内在无序蛋白 (IDP) 通过相分离驱动生物分子凝聚物形成.
粗粒度 (CG) 模拟对于研究IDP相分离至关重要.
目前的Cα-only模型在表示骨相互作用和二次结构方面缺乏准确性.

研究的目的:

引入混合分辨率 (HyRes) 蛋白质模型,以提高IDP相隔模拟的准确性.
评估HyRes捕获骨干介导的相互作用和短暂的二次结构的能力.
评估HyRes在模拟自发相位分离和突变效应方面的效率和准确性.

主要方法:

开发了一种混合分辨率 (HyRes) 模型,具有原子骨干和粗粒度侧链.
使用HyRes模拟GY-23蛋白质的自发相分离.
研究单个氨基酸突变 (His到Lys) 对相分离的影响.
使用HyRes分析TDP-43的相分离,重点关注保存区域 (CR) 的疾病相关突变.

主要成果:

HyRes准确地模拟了单体IDP螺旋倾向和链条尺寸.
模拟成功捕捉了GY-23的自发相位分离和突变效应.
根据实验数据,HyRes预测凝结物中β结构的增加.
在HyRes模拟中,重新总结了TDP-43 CR突变对螺旋性和相分离倾向的影响.
分析表明,脊柱和侧链相互作用的平衡,而不是单独的螺旋性,决定了相隔.

结论:

HyRes是模拟IDP相分离的有效蛋白质模型.
该模型准确地捕捉了短暂的二次结构对相位分离的影响.
HyRes有助于更深入地了解蛋白质结构和相隔现象之间的相互作用.

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