Topological analysis of morphological changes of proteins due to the differences of experimental conditions of X-ray structural analysis

In structural biology, it is an important problem how tiny local mutation of the protein affect its global structure. To understand the mechanism, we focus on a topological method called “Fatgraph models of proteins” [1]. The model is a topological two-manifold with boundary components (surface) which have one to one correspondence with three-dimensional protein structures listed on Protein Data Bank (PDB) [2] with several exceptions. The traits of each surface for each protein are described by invariants.

Although the model enables us to grasp the global structure of each protein, it is still unclear if the method is useful for comparison between several structures because there was no research on the effect of the differences of experimental conditions on protein structure.

Here, we investigated the effect of experimental conditions of X-ray analysis and the fatgraph invariants of proteins which share identical sequences. We found that the invariants are sensitive to the differences of the conditions and proposed a method to analyse the morphological changes due to the mutation.


[1] R. C. Penner, et al., (2010), Comm. Pure Appl. Math. Volume 63 , Issue 10 , 1249 - 1297.
[2] H.M. Berman, et al. (2000), The Protein Data Bank, Nucleic Acids Res, 28: 235 - 242. http://www.rcsb.org/