Abstract
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.
Highlights
According to McPherson[1], the first observation of a protein crystal - earthworm hemoglobin - is about 150 years old[2]
Since the weak contacts are not considered in the multilevel topological analysis, the topologies obtained by the two methods can be assumed to be comparable
Coordination numbers are very often much lower in protein crystals, in agreement with the fact that a considerable fraction of their volume is occupied by liquid water
Summary
Since packing contacts were determined with two different approaches in protein crystals (‘Distance method’, see Methods) and in small molecule crystals (‘Domains method’), it is mandatory to compare the results obtained by following these two different approaches and to verify that they produce identical results. Only 6% of the protein crystals are associated with the most frequent topology (fcu) and only 19% of them have one of the four most common topologies (fcu, bct, hex, vcs). This suggests that the suboptimal packing of the protein molecules in the crystal state allows a wider number of topologies and none of them can be much more frequent than the others. The underlying nets of crystals of monomeric proteins where the asymmetric unit contains two independent molecules set are very diverse and it was impossible to separate any preferable motif (Table 2)
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