Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
Structure. 2011 Apr 13;19(4):523-33. doi: 10.1016/j.str.2011.01.015.
Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms.
大多数当前的晶体学结构精修方法通过使用先验信息来增强衍射数据，这些先验信息包括基于泡利不相容原理的键、角、二面角、平面约束和原子斥力。然而，静电和范德华吸引力是提供额外先验信息的物理力。在这里，我们评估了将静电纳入用于全原子（包括氢）联合中子/ X 射线精修的力场。使用不包括静电或包括静电的力场，对两个 DNA 和一个蛋白质晶体结构进行了联合中子/ X 射线衍射数据集的精修。氢键取向/几何形状有利于包含静电。对 Z-DNA 进行静电精修导致了对 Z-DNA 熵稳定化的假设，这可能部分解释了将 DNA 的 B 形式转化为 Z 形式的热力学。因此，包含静电有助于联合中子/ X 射线精修，特别是对于放置和定向氢原子。
