Department of Chemistry, University of Pavia, viale Taramelli 12, I-27100, Pavia, Italy.
Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria.
Sci Rep. 2017 Oct 16;7(1):13209. doi: 10.1038/s41598-017-12699-4.
We compared the topologies of protein and small molecule crystals, which have many common features - both are molecular crystals with intermolecular interactions much weaker than intramolecular interactions. They also have different features - a considerably large fraction of the volume of protein crystals is occupied by liquid water while no room is available to other molecules in small molecule crystals. We analyzed the overall and local topology and performed multilevel topological analyses (with the software package ToposPro) of carefully selected high quality sets of protein and small molecule crystal structures. Given the suboptimal packing of protein crystals, which is due the special shape and size of proteins, it would be reasonable to expect that the topology of protein crystals is different from the topology of small molecule crystals. Surprisingly, we discovered that these two types of crystalline compounds have strikingly similar topologies. This might suggest that molecular crystal formations share symmetry rules independent of molecular dimension.
我们比较了蛋白质晶体和小分子晶体的拓扑结构，它们有许多共同特征——都是分子晶体，分子间相互作用比分子内相互作用弱得多。它们也有不同的特点——蛋白质晶体的相当大一部分体积被液态水占据，而小分子晶体中没有其他分子的空间。我们分析了整体和局部拓扑结构，并对精心挑选的高质量蛋白质和小分子晶体结构数据集进行了多层次拓扑分析（使用 ToposPro 软件包）。考虑到蛋白质晶体的包装不理想，这是由于蛋白质的特殊形状和大小，我们有理由预期蛋白质晶体的拓扑结构与小分子晶体的拓扑结构不同。令人惊讶的是，我们发现这两种类型的结晶化合物具有惊人相似的拓扑结构。这可能表明分子晶体的形成共享独立于分子尺寸的对称规则。
