Developing New Applications for Perturbation Response Scanning Method to Study Conformational Modulation of Globular Proteins

Official URL: https://risc01.sabanciuniv.edu/record=b2553762 _(Table of contents)

Conformational transitions in proteins facilitate precise physiological functions. Therefore, it is crucial to understand the mechanisms underlying these processes to modulate protein function. Yet, studying structural and dynamical properties of proteins are notoriously challenging due to the complexity of the underlying potential energy surfaces (PES). Perturbation Response Scanning (PRS) method has previously been developed to identify key residues that participate in the communication network responsible for specific conformational transitions. PRS is based on a residue-by-residue scan of the protein to determine the subset of residues/forces which provide the closest conformational change leading to a target conformational state, inasmuch as linear response theory applies to these motions. In this thesis, two novel methods are developed to further explore the dynamics of proteins. Perturb-Scan-Pull (PSP) method evaluates if conformational transitions may be triggered on the PES. It aims to study functionally relevant conformational transitions in proteins using results obtained by PRS and feeding them as inputs to steered molecular dynamics simulations. The success and the transferability of the method are evaluated on three protein systems having different complexity of motions on the PES: calmodulin, adenylate kinase, and bacterial ferric binding protein. Results indicate that PSP method captures the target conformation, while providing key residues and the optimum paths with relatively low free energy profiles. Unlike PSP method, which is developed to study conformational changes between two known states of a protein and considers the best force vector toward the target state, protein perturbation responses can be clustered with the hope of exploring the collective variables (CV) toward new conformations of a protein. The perturbation response clustering (PRC) technique is developed to study the alternative conformations available to proteins for which these have not yet been detected via experimental methods. Using collective variables predicted via clustering of the response vectors, new conformations are sampled, which capture low lying energy states that exist under specific circumstances in vivo. The methodologies developed in this thesis can be applied on a wide range of proteins having different functions and displaying various types of motions. More importantly, these methods can be extended to study nucleic acids (DNA, RNA) or membrane proteins by considering lipids molecules.