Protein structures can be studied as complex networks of interacting amino acids. I have studied proteins of different structural classes from the network perspective. The results of this study indicate that proteins, regardless of their structural class, show small-world network property. I discovered that contrary to most other complex networks protein contact networks are of assortative nature. Moreover I was able to associate the observed assortative nature to kinetics of folding. I am pondering on the possible implications of these results and the questions that they pose.

• • Ganesh Bagler and Somdatta Sinha, “Assortative mixing in protein Contact Networks and protein folding kinetics”, Bioinformatics, 23, 14, 1760—1767 (2007). Bioinformatics | PDF | arxiv.org/abs/0711.2723

  • Ganesh Bagler and Somdatta Sinha, "Network properties of protein Structures", Physica A, 346, 27-33 (2005). Physica A | arXiv:q-bio.MN/0408009

Enzyme Engineering

We recently published a research reporting graph theoretical studies of a plant Cu,Zn SOD structure and engineering a thermostable enzyme by mutagenesis that were predicted by computational modeling. This study suggests the importance of increased monomer to dimer ratio to enhance thermostability of Cu,Zn SOD, wherein mutation of a free cysteine (Cys-95) played a central role. The results were supported by in silico as well as other biochemical parameters. The engineered SOD can be used for developing transgenic plants tolerant to abiotic stresses, particularly for high temperature and drought stress, where the temperature can rise to as high as 50–60°C.

Arun Kumar, Som Dutt, Ganesh Bagler, Paramvir Singh Ahuja and Sanjay Kumar, "Engineering a thermo-stable superoxide dismutase functional at sub-zero to 50°C, which also tolerates autoclaving." Scientific Reports (Nature Publication Group), 2, 387 (2012). DOI:10.1038/srep00387