Dynamics Of Protein Structure Network: From Equilibrium
And Unfolding Simulations On Lysozyme.
Saraswathi Vishveshwara
Molecular Biophysics unit, Indian Institute of Science, Bangalore, India 560012
The three-dimensional structure of proteins have been recently investigated
from network perspective, where the amino acid residues are considered as the nodes in
the network and the non-covalent interactions between them is considered for the edgeformation (Brinda and Vishveshwara, Biophysical Journal, 89(6), 4159-70, 2005). It was
demonstrated that the Protein Structure Graphs (PSG) exhibit a complex network
behaviour, which depends on the strength of the non-covalent interaction. Here, the
dynamical behaviour of such networks has been examined by considering the example of
T4-lysozyme. The equilibrium dynamics and the process of unfolding is followed by
simulating the protein with explicit water molecules at 300K and at 500K
respectively. The snapshots of the protein structure from the simulations are represented
as Protein Structure Graphs of non-covalent interactions. A critical strength of interaction
(Icritical) for the transition of the largest cluster size has been identified. The equilibrium
properties of the network parameters such as the size and the composition of the largest
cluster and hubs and their locations in the three dimensional structure of the protein have
been evaluated from the 300K simulation. The network changes that take place during
unfolding, have been monitored from the 500K simulations. Such an analysis
provides insights into the details of the changes occurring in the protein tertiary structure
at the level of amino acid side-chain interactions and can prove to be a valuable method
to identify residues important for the stability and folding of proteins.