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活性部位在斯特雷普塔维丁/生物素复合体形成中的作用

Nupur Bansal¹, Zheng Zheng¹, Lin Frank Song¹

¹Department of Chemistry and Department of Biochemistry and Molecular Biology , Michigan State University , 578 South Shaw Lane , East Lansing , Michigan 48824 , United States.

Journal of the American Chemical Society

|April 3, 2018

概括

了解蛋白的运动是基于结构的药物设计的关键. 这项研究介绍了MT_Flex-b,用于绘制配置并计算自由能量,进步抑制剂和蛋白质设计.

科学领域:

计算化学
结构生物学
生物物理

背景情况:

蛋白质活性部位的飞运动会影响基质的结合,这对药物设计至关重要.
现有的方法缺乏对膜动态及其对连接体相互作用的影响的详细见解.

研究的目的:

开发和验证一种计算方法 (MT_Flex-b) 来分析蛋白的运动及其对结合的影响.
产生蛋白质配置状态并估计与动态相关的自由能量景观.
将工作流应用于链素/生物素系统进行验证.

主要方法:

使用MT_Flex-b方法在分子能量格局上生成蛋白配置状态.
使用可移动类型 (MT) 自由能量方法来估计自由能量变化.
通过与分子动力学 (MD) 模拟和实验结合自由能数据进行比较来验证结果.

主要成果:

通过在apo和holo状态下考虑循环_3-4的灵活性,成功生成了斯特雷普塔维丁/生物素系统的自由能量表面.
估计斯特雷普塔维丁/生物素的结合自由能量大约为-16.2 kcal/mol,与实验值-18.3 kcal/mol相当.
在MT_Flex-b/MT方法,MD模拟和实验数据之间显示出强烈的一致性.

结论:

与MT方法相结合的MT_Flex-b方法有效地提供了对蛋白运动的独特见解.
这一战略为推进基于结构的药物设计和蛋白质工程应用提供了巨大的潜力.
验证的方法可应用于各种系统,包括酶,HSP90和HIV蛋白酶.

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