Effects of artificial mutations on topological features of proteins

Relationship between the mutations of the proteins and its physiological activities is an important research area for many reasons. One reason is that bacteria or viruses acquire their resistance to existing drugs by mutations. The conformational changes due to the mutations have a significant role on the affinitiy to their ligand.

To understand the relationships, we focus on a topological method called “Fatgraph models of proteins” [1]. Fatgraph models of proteins are 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 only a few exceptions. Topological invariants represent geometrical features, and thus they are effective method to grasp the effects of local mutations on three dimensional structures of the proteins as a whole.

In this research we investigated the topological features of artificial proteins and showed the topological traits of mutants which have a drug resisitant to antibiotics.

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