Studying allosteric modulation of the conformational dynamics of proteins using Perturbation Response Scanning (PRS) method

The dynamic nature of the proteins give rise to a variety of conformations which are relevant to their biological functions. Conformational changes can be defined as an exchange between main structure states. Studying the structural and biophysical properties of these states are challenging because of the complexity of the information they contain.  Perturbation Response Scanning (PRS) method could be considered as an promising approach to study conformational dynamics of proteins. The goal of this project is to investigate the potential residues/areas of proteins capable of modulating conformational changes (allosteric site). To this aim, PRS will be applied to identify key residues of different proteins and results comparatively evaluated with experimental data.
Students willing to participate in this project will work on : 1. Literature Review and Research Design  2. Molecular simulations Using NAMD (Scalable Molecular Dynamics) 3. PRS calculation 4. Result analysis.