基准测试自由能量计算:对两个蛋白质系统的两个模拟软件平台的单个和双重突变进行分析
Shivani Gupta1,2, Qinfang Sun1,2, Ronald M Levy1,2
1Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA, USA.
bioRxiv : the preprint server for biology
|November 24, 2025
概括
自由能量扰动 (FEP) 模拟可以准确预测突变导致的蛋白质稳定性变化. 施罗丁格和GROMACS软件平台在计算S核酶和T4溶酶单个和双重突变的自由能量变化方面都表现出高可靠性.
科学领域:
- 计算生物学和生物信息学
- 蛋白质工程和设计
- 分子动力学模拟模型
背景情况:
- 蛋白质的稳定性和适应性受到突变的关键影响.
- 了解序列结构功能关系是蛋白质分析的关键.
- 自由能量扰动 (FEP) 是一种计算方法,用于量化突变效应.
研究的目的:
- 为了比较施罗丁格和GROMACS FEP模拟的准确性和可靠性.
- 评估对S核酶和T4溶酶的突变诱导的自由能量变化 (ΔG) 的预测.
- 评估FEP在预测双重突变非添加性方面的表现.
主要方法:
- 利用单个和双重突变的自由能量扰动 (FEP) 模拟.
- 使用OPLS4力场的施罗丁格和使用Amber99SB-ILDN力场的GROMACS.
- 与实验数据比较计算的Δ和非附加性值.
主要成果:
- 在计算和实验之间观察到高相关性 (Pearson r > 0.80),用于使用两个平台的S.核酶和T4溶酶的单个突变.
- 施罗丁格和GROMACS与双重突变自由能量变化 (皮尔森r = 0.74) 和非添加性 (皮尔森r = 0.79) 的实验数据有很好的一致性.
- 对于单个和双重突变,Schrödinger和GROMACS计算的值之间发现了强烈的相关性.
结论:
- 施罗丁格FEP+和GROMACS是预测突变诱导的自由能量变化的高效可靠工具.
- 经过实验验证的FEP模拟,为量化蛋白质热稳定性的变化提供了一个强大的框架.
- 这种方法是推进蛋白质工程和设计策略的宝贵工具.
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