Fabiola Felcy, Bertram Richard, Korostelev Andrei, Chapman Michael S
Kasha Laboratory of Biophysics, Florida State University, Tallahassee, Florida 32306-4380, USA.
Protein Sci. 2002 Jun;11(6):1415-23. doi: 10.1110/ps.4890102.
A new semi-empirical force field has been developed to describe hydrogen-bonding interactions with a directional component. The hydrogen bond potential supports two alternative target angles, motivated by the observation that carbonyl hydrogen bond acceptor angles have a bimodal distribution. It has been implemented as a module for a macromolecular refinement package to be combined with other force field terms in the stereochemically restrained refinement of macromolecules. The parameters for the hydrogen bond potential were optimized to best fit crystallographic data from a number of protein structures. Refinement of medium-resolution structures with this additional restraint leads to improved structure, reducing both the free R-factor and over-fitting. However, the improvement is seen only when stringent hydrogen bond selection criteria are used. These findings highlight common misconceptions about hydrogen bonding in proteins, and provide explanations for why the explicit hydrogen bonding terms of some popular force field sets are often best switched off.
一种新的半经验力场已被开发出来，用于描述具有方向分量的氢键相互作用。氢键势支持两个备选目标角度，这是基于羰基氢键受体角度呈双峰分布的观察结果。它已被实现为一个大分子精修程序包的模块，以便在大分子的立体化学受限精修中与其他力场项相结合。氢键势的参数经过优化，以最佳拟合来自多个蛋白质结构的晶体学数据。使用这种额外约束对中等分辨率结构进行精修会得到改进的结构，同时降低自由R因子和过拟合。然而，只有在使用严格的氢键选择标准时才能看到这种改进。这些发现突出了关于蛋白质中氢键的常见误解，并解释了为什么一些流行力场集的显式氢键项通常最好关闭。
