Abstract

Orientation of water molecules in the vicinity of the globular protein SNase is studied. It is shown that two types of characteristic orientations can be distinguished among molecules in direct contact with the protein. Approximately 44% of these molecules are oriented by their OH vector towards the nearest protein atom forming a donor hydrogen bond; 20% of them are directed by their oxygen towards the nearest atom while their protons are directed mainly away from the protein. By forming a network of hydrogen bonds with other water molecules, these molecules initiate orientation correlations in the protein environment within a region of 0.45 nm. More distant water molecules are arranged randomly with respect to the protein. The orientation is described by the angle between vector N directed from the water molecule to the nearest protein atom and characteristic vectors of the water molecule (directions OH, OL, and dipole moment D). A more detailed information about orientations is retrieved from a two-dimensional distribution diagram P(cos(θ), φ) representing direction N in a spherical coordinate system associated with the water molecule. The diagram provides an unambiguous description for the orientation of water molecules and allows a quantitative calculation of the fraction of molecules with a specified orientation.

中文翻译：

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球状蛋白质附近水分子的取向

摘要

研究了球状蛋白质 SNase 附近水分子的取向。结果表明，在与蛋白质直接接触的分子之间可以区分两种类型的特征取向。大约 44% 的这些分子通过它们的 OH 载体朝向最近的蛋白质原子定向，形成供体氢键；它们中的 20% 被它们的氧导向最近的原子，而它们的质子主要远离蛋白质。通过与其他水分子形成氢键网络，这些分子在 0.45 nm 区域内的蛋白质环境中启动取向相关性。更远的水分子相对于蛋白质随机排列。方向由向量N之间的角度描述从水分子指向最近的蛋白质原子和水分子的特征向量（方向OH、OL和偶极矩D）。从表示与水分子相关的球面坐标系中的方向N的二维分布图P (cos(θ), φ) 中检索有关方向的更详细信息。该图为水分子的方向提供了明确的描述，并允许定量计算具有指定方向的分子的分数。