Research Projects

The research aims to predict the regions that unfold first and the sequence of non-covalent bond-breaking from the crystal structure of proteins. The study will use a spring network to represent the protein as a spring network obtained from its native structure, identifying soft spots that are more susceptible to unfolding. The differences in behavior of a network with identical springs and sequence dependent springs will show the effects of elastic heterogeneity. The evolution of redundant bonds and soft spots during the unfolding process will be studied to explain the cooperative nature of bond breaking, resulting in a gradual or sudden loss of rigidity or the formation of intermediates. The shear and bulk modulus as a function of the mean coordination number will be used to analyze the rigidity transition. The study will focus on Hemoglobin, Trypsin, HIV-1 protease, Myoglobin, and Barnase, with molecular dynamics simulations performed for other proteins. The significance of this research is that it will provide target sites for drugs and identify mutations that make the protein unstable. It will also lead to the development of synthetic proteins that are robust to unfolding and provide a framework to apply the well-studied field of network glasses to the structural transitions in proteins.