Held Jeanette, van Smaalen Sander
Laboratory of Crystallography, University of Bayreuth, D-95440 Bayreuth, Germany.
Acta Crystallogr D Biol Crystallogr. 2014 Apr;70(Pt 4):1136-46. doi: 10.1107/S1399004714001928. Epub 2014 Mar 21.
Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM; Bader (1994), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254-1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337-351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C-H...O hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.
基于巴德分子中原子的量子理论[QTAIM；巴德（1994年），《分子中的原子：量子理论》。牛津大学出版社]，对鸡蛋清溶菌酶（HEWL）活性位点的化学键进行了分析，该理论应用于从多极模型导出的电子密度图。观察发现，在100 K温度下HEWL的原子位移参数（ADP）大于298 K时小生物分子晶体中的ADP。这一特征表明，HEWL冷晶体中的ADP反映的是冻结无序，而非原子的热振动。直接推广小分子晶体多极研究的结果，蛋白质晶体电子密度分析的重要结果是，在结构精修中多极参数不能以有意义的方式独立变化。相反，通过根据王及其同事的X射线衍射数据[王等人（2007年），《晶体学报》D63，1254 - 1268]精修原子坐标和ADP，开发了一种HEWL的多极模型，而多极参数固定为来自ELMAM2数据库[多马加拉等人（2012年），《晶体学报》A68，337 - 351]的可转移多极参数值。给出了基于该多极模型的静态和动态电子密度。根据QTAIM对其拓扑性质的分析表明，共价键具有与小分子共价键相似的性质。确定了Glu35和Asp52残基的中等强度氢键，它们被认为是HEWL活性位点的重要组成部分。此外，通过多极电子密度中键临界点（BCP）的存在，确定了一系列弱C-H...O氢键。有人提出，这些弱相互作用可能对定义HEWL的三级结构和活性很重要。Glu35的去质子化状态使得无法区分菲利普斯机制和科什兰德机制。
