在使用量子力学/分子力学和机器学习潜能的联合量子力学/分子力学和机器学习潜力的关氨-提氨 (G-T) 不对对对的质子转移反应上,电子和核量子效应
Yujun Tao1, Timothy J Giese1, Darrin M York1
1Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
Molecules (Basel, Switzerland)
|June 19, 2024
概括
通过质子转移形成罕见的关氨酸-丁氨酸 (G-T) DNA 异对. 核量子效应显著降低了G-T共聚的能量障碍,有助于实验数据的解释.
科学领域:
- 生物物理学的生物物理.
- 计算化学计算化学
- 分子生物学分子生物学
背景情况:
- 罕见的核基相对体可以导致沃森-克里克 (WC-like) 样的DNA错配.
- 在 tautomerization 期间的质子转移是快速的,并且在实验上具有挑战性.
- 之前的NMR研究表明,存在过渡性WC类的关氨酸-丁氨酸 (G-T) 误对.
研究的目的:
- 调查G-T误对复合的机制和核量子效应.
- 模拟一个B-DNA螺旋与一个摇摆的关氨酸-丁氨酸 (wGT) 错配.
- 开发用于准确计算自由能量屏障的计算方法.
主要方法:
- 进行了ab initio量子力学/分子力学 (QM/MM) 模拟.
- 开发了一个QM/MM机器学习潜力校正 (QM/MM-ΔMLP) 进行增强采样.
- 利用途径积分分子动力学来包括核量子效应.
主要成果:
- QM/MM模拟需要广泛采样,以获得精确的自由能源障碍.
- QM/MM-ΔMLP显著提高了计算效率和可访问的时间表.
- 核量子效应对分体化途径产生了适度的影响,但降低了自由能量屏障.
结论:
- 这项研究合理化了G-T不匹配的实验观测.
- 预测罕见核基 tautomers 的种群和它们在 B-DNA 中的相互转换率.
- 突出了核量子效应在DNA基配对动态中的重要性.
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