Kodandapani R, Vijayan M
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
Acta Crystallogr D Biol Crystallogr. 1993 Mar 1;49(Pt 2):234-45. doi: 10.1107/S090744499200653X.
Low-humidity monoclinic lysozyme, resulting from a water-mediated transformation, has one of the lowest solvent contents (22% by volume) observed in a protein crystal. Its structure has been solved by the molecular replacement method and refined to an R value of 0.175 for 7684 observed reflections in the 10-1.75 A resolution shell. 90% of the solvent in the well ordered crystals could be located. Favourable sites of hydration on the protein surface include side chains with multiple hydrogen-bonding centres, and regions between short hydrophilic side chains and the main-chain CO or NH groups of the same or nearby residues. Major secondary structural features are not disrupted by hydration. However, the free CO groups at the C terminii and, to a lesser extent, the NH groups at the N terminii of helices provide favourable sites for water interactions, as do reverse turns and regions which connect beta-structure and helices. The hydration shell consists of discontinuous networks of water molecules, the maximum number of molecules in a network being ten. The substrate-binding cleft is heavily hydrated, as is the main loop region which is stabilized by water interactions. The protein molecules are close packed in the crystals with a molecular coordination number of 14. Arginyl residues are extensively involved in intermolecular hydrogen bonds and water bridges. The water molecules in the crystal are organized into discrete clusters. A distinctive feature of the clusters is the frequent occurrence of three-membered rings. The protein molecules undergo substantial rearrangement during the transformation from the native to the low-humidity form. The main-chain conformations in the two forms are nearly the same, but differences exist in the side-chain conformation. The differences are particularly pronounced in relation to Trp 62 and Trp 63. The shift in Trp 62 is especially interesting as it is also known to move during inhibitor binding.
由水介导的转变产生的低湿度单斜晶型溶菌酶，其溶剂含量是蛋白质晶体中观察到的最低值之一（体积分数为22%）。其结构已通过分子置换法解析，并针对10 - 1.75 Å分辨率壳层中的7684个观测反射精修至R值为0.175。有序晶体中90%的溶剂可被定位。蛋白质表面有利的水合位点包括具有多个氢键中心的侧链，以及短亲水侧链与相同或附近残基的主链羰基或氨基之间的区域。主要二级结构特征不会因水合作用而破坏。然而，C末端的游离羰基以及螺旋N末端的氨基（程度稍低）为水相互作用提供了有利位点，反向转角以及连接β结构和螺旋的区域也是如此。水合壳由不连续的水分子网络组成，一个网络中水分子的最大数量为十个。底物结合裂隙被大量水合，通过水相互作用稳定的主环区域也是如此。蛋白质分子在晶体中紧密堆积，分子配位数为14。精氨酸残基广泛参与分子间氢键和水桥的形成。晶体中的水分子被组织成离散的簇。这些簇的一个显著特征是频繁出现三元环。蛋白质分子在从天然形式转变为低湿度形式的过程中经历了大量重排。两种形式的主链构象几乎相同，但侧链构象存在差异。这些差异在色氨酸62和色氨酸63处尤为明显。色氨酸62的移动特别有趣，因为已知它在抑制剂结合过程中也会移动。
