使用统计数据和QM/MM计算研究揭示了素键和键的首选微环境
Liping Zhou1,2, Jintian Li1,2, Yulong Shi1,2
1Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. zjxu@simm.ac.cn.
Physical chemistry chemical physics : PCCP
|June 27, 2023
概括
素键 (XBs) 喜欢疏水性蛋白质微环境而不是键 (HBs). 这项研究使用局部疏水性和介电常数来量化这些偏好,这对于药物设计至关重要.
科学领域:
- 生物化学 生物化学
- 计算化学计算化学
- 结构生物学 结构生物学
背景情况:
- 键 (HBs) 和键 (XBs) 是分子识别和药物设计中的关键非共价相互作用.
- 蛋白质结构异质,影响HBs和XBs与连接体的形成.
- 缺乏对蛋白质微环境对HB和XB形成的影响的系统研究.
研究的目的:
- 使用局部疏水性 (LHs) 和局部介电常数 (LDCs) 量化描述蛋白质微环境.
- 探索蛋白质 - 配体复合体内HBs和XBs的微环境偏好.
- 为了比较HBs和XBs在不同的微环境中的行为.
主要方法:
- 定义的LH和LDC用于描述蛋白质微环境.
- 进行了对22,011个配体蛋白结构的数据库调查.
- 分析了91,966个HBs和1,436个XBs.
- 执行了量子力学-分子力学 (QM/MM) 的计算.
主要成果:
- 与HBs相比,XBs对疏水的微环境有显著的偏好.
- 极地残留物 (例如ASP) 有利于HBs,而非极地残留物 (例如PHE,MET) 有利于XBs.
- XBs的LH和LDC (8.86±4.00) 比HBs (10.69±4.36) 低,表明他们更喜欢极地较小的环境.
- QM/MM计算显示,与真空相比,微环境中的HBs和XBs的相互作用能量减少.
- 在介电常数差异较大的环境中,HB强度比XB强度明显受损.
结论:
- 蛋白质微环境对HBs和XBs的形成和强度有很大影响.
- XBs在疏水口袋中更为普遍,而HBs在极地残留附近更为普遍.
- 了解这些微环境偏好对于准确的强度评估和合理的药物设计至关重要.
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