Brünger A T, Karplus M
Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138.
Proteins. 1988;4(2):148-56. doi: 10.1002/prot.340040208.
A method for the prediction of hydrogen positions in proteins is presented. The method is based on the knowledge of the heavy atom positions obtained, for instance, from X-ray crystallography. It employs an energy minimization limited to the environment of the hydrogen atoms bound to a common heavy atom or to a single water molecule. The method is not restricted to proteins and can be applied without modification to nonpolar hydrogens and to nucleic acids. The method has been applied to the neutron diffraction structures of trypsin, ribonuclease A, and bovine pancreatic trypsin inhibitor. A comparison of the constructed and the observed hydrogen positions shows few deviations except in situations in which several energetically similar conformations are possible. Analysis of the potential energy of rotation of Lys amino and Ser, Thr, Tyr hydroxyl groups reveals that the conformations of lowest intrinsic torsion energies are statistically favored in both the crystal and the constructed structures.
本文提出了一种预测蛋白质中氢原子位置的方法。该方法基于例如从X射线晶体学获得的重原子位置信息。它采用能量最小化方法，且仅限于与共同重原子或单个水分子结合的氢原子的环境。该方法不限于蛋白质，可直接应用于非极性氢原子和核酸。该方法已应用于胰蛋白酶、核糖核酸酶A和牛胰蛋白酶抑制剂的中子衍射结构。对构建的氢原子位置与观察到的氢原子位置进行比较，结果表明，除了存在几种能量相似构象的情况外，两者几乎没有偏差。对赖氨酸氨基以及丝氨酸、苏氨酸、酪氨酸羟基的旋转势能分析表明，在晶体结构和构建结构中，具有最低固有扭转能的构象在统计学上都更受青睐。
