Anderson D H, Weiss M S, Eisenberg D
Molecular Biology Institute Department of Chemistry and Biochemistry and UCLA-DOE Lab of Structural Biology and Molecular Medicine, University of California, Los Angeles, CA 90095-1570, USA.
J Mol Biol. 1997 Oct 24;273(2):479-500. doi: 10.1006/jmbi.1997.1318.
A detailed description is given of the structure of the small protein mating pheromone Er-1 at atomic resolution. Emphasis is placed on the locations of charges and hydrogen bonds. The model includes all the protein atoms, anisotropic displacement parameters, four disordered side chains, 22 water molecules, a disordered ethanol, and "riding" hydrogen atoms. Analysis of the model revealed that this dense crystal is perfused by hydrogen-bonding networks of solvent and protein atoms. The termini of helices are capped by hydrogen bonding to solvent and protein atoms, and to symmetry-related molecules. An examination of the valencies and charges of the hydrogen-bonding groups suggests that three of the "water" molecules capping the C termini of two helices, and one other, may instead be NH4 ions. Water molecules mediate all but one of the interhelical hydrogen bonds, and many of the lattice interactions. Regions of the molecule where the atomic vibrations deviate from isotropy are identified. There is almost no overall libration of the molecule allowed by the packing, but the side-chains vibrate relative to the backbone. Four side-chains display alternate conformations. Indirect evidence is presented that the switches between their conformations are correlated and driven by protonation of acidic side-chains. These structural features are discussed in the context of function and stability. Equipped with the analysis of the model, we review the course and results of the refinement of the model against 1 A X-ray diffraction data to a crystallographic R-factor of 12.92%.
本文给出了小分子蛋白质交配信息素Er-1在原子分辨率下的结构详细描述。重点关注了电荷和氢键的位置。该模型包括所有蛋白质原子、各向异性位移参数、四条无序侧链、22个水分子、一个无序乙醇分子以及“游动”氢原子。对该模型的分析表明，这种致密晶体被溶剂和蛋白质原子的氢键网络贯穿。螺旋的末端通过与溶剂、蛋白质原子以及对称相关分子形成氢键而被封闭。对氢键基团的化合价和电荷的研究表明，封端两条螺旋C末端的三个“水”分子以及另一个分子可能是NH₄⁺离子。除了一条螺旋间氢键外，其他所有螺旋间氢键以及许多晶格相互作用均由水分子介导。确定了分子中原子振动偏离各向同性的区域。堆积几乎不允许分子整体摆动，但侧链相对于主链振动。四条侧链呈现交替构象。有间接证据表明，它们构象之间的转换是相关的，并且由酸性侧链的质子化驱动。结合功能和稳定性对这些结构特征进行了讨论。基于对该模型的分析，我们回顾了根据1 Å X射线衍射数据将模型精修至晶体学R因子为12.92%的过程和结果。
