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使用分子溶解理论预测离子和水与核酸的结合方式

George M Giambaşu¹, David A Case¹, Darrin M York^1,2,3

¹Department of Chemistry and Chemical Biology , Rutgers, The State University of New Jersey , New Brunswick , New Jersey 08901 , United States.

Journal of the American Chemical Society

|January 12, 2019

概括

预测离子和水与核酸的结合对于理解它们的功能至关重要. 本研究引入了使用3D-RISM理论的计算工具,以准确预测G-四重复结构中的特定离子结合.

科学领域:

计算生物物理
分子动力学
结构生物学

背景情况:

特定位置的离子和水结合会影响核酸折叠,动态和功能.
在计算上预测这种局部结合仍然是一个重大挑战.

研究的目的:

开发和验证用于预测离子和水位与核酸结合的计算工具.
应用工具集来分析Oxytricha nova的G-四重体 (Oxy-GQ) 的离子结合.

主要方法:

使用3D-RISM分子溶解理论与拓分析相结合.
使用皇冠乙烯和离子通道的数据,精制和验证了氧参数.
应用验证的参数来研究Oxy-GQ在不同盐条件下的阴离子占用率.

主要成果:

3D-RISM方法准确地预测了Oxy-GQ中的和水结合点,与晶体学数据一致.
精确的参数改善了Oxy-GQ中心通道中的阴离子占用率预测.
开发的参数证明适用于多种生物系统.

结论:

这项研究提出了一种验证的计算方法,用于预测特定位置离子与核酸的结合.
这些发现提供了关于离子大气对G四重体结构和功能的影响的见解.
未来的工作旨在扩展该方法以预测双价离子结合.

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