Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models
Highly designable structures can be distinguished based on certain geometric graphical features of the interactions confirming the fact that the topology of a protein structure and its residue-residue interaction network are important determinants of its designability. The most designable structures and poorly designable structures obtained for sets of proteins having the same number of residues are compared, and it is shown that the most designable structures predicted by the graph features of the contact diagrams are more densely packed whereas the poorly designable structures are more open loop type structures or structures that are loosely packed. Interestingly enough, it can also be seen that these highly designable structures obtained are also common structural motifs found in nature.
KeywordsDesignability Contact maps Graph features
Unable to display preview. Download preview PDF.
- 3.Cejtin, H., Edler, J., Gottlieb, A., Helling, R., Li, H., Philbin, J., Wingreen, N., Tang, C.: Fast tree search for enumeration of a lattice model of protein folding. Journal of Chemical Physics 116 (2002)Google Scholar
- 5.Yang, J.-Y., Yu, Z.-G., Anh, V.: Correlations between designability and various structural characteristics of protein lattice models. Journal of Chemical Physics 126 (2007)Google Scholar
- 6.Melin, R., Li, H., Wingreen, N.S., Tang, C.: Designability, thermodynamic stability, and dynamics in protein folding: A lattice model study. Journal of Chemical Physics 110 (1999)Google Scholar
- 21.Krishnan, A., Zbilut, J.P., Tomita, M., Giuliani, A.: Proteins as networks: Usefulness of graph theory in protein science. Current Protein and Peptide Science 9 (2008)Google Scholar
- 27.Kannan, N., Selvaraj, S., Gromiha, M.M., Vishveshwara, S.: Clusters in alpha/beta barrel proteins: implications for protein structure, function, and folding: a graph theoretical approach. Proteins 43 (2001)Google Scholar
- 32.Leelananda, S.P., Towfic, F., Jernigan, R.L., Kloczkowski, A.: Exploration of the relationship between topology and designability of conformations. Journal of Chemical Physics 134 (2011)Google Scholar
- 35.Lipman, D.J., Wilbur, W.J.: Modeling Neutral and Selective Evolution of Protein Folding. Proceedings of the Royal Society of London Series B-Biological Sciences 245 (1991)Google Scholar
- 36.Vendruscolo, M., Dokholyan, N.V., Paci, E., Karplus, M.: Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E 65 (2002)Google Scholar
- 37.Hall, M., Frank, E., Holmes, G., Pfahringer, B., Reutemann, P., Witten, I.H.: The WEKA Data Mining Software: An Update. SIGKDD Explorations 11 (2009)Google Scholar