Solvation Thermodynamics and Free Energy Surfaces of Intrinsically Disordered Proteins (IDPs) in Aqueous Solutions

Contrary to the traditional structure-function paradigm for proteins, intrinsically disorderedproteins (IDPs) and regions (IDRs) are highly disordered sequences that lack a fixed crystal structure yet perform various biological activities such as cell signaling, regulation, and recognition. The interactions of these disordered regions with water molecules are essential in the conformational distribution. Hence, exploring their solvation thermodynamics is crucial for understanding their functions, which are challenging to study experimentally. In this thesis, classical Molecular Dynamics (MD), 3D-Two Phase Thermodynamics (3D- 2PT), and umbrella sampling have been employed to gain insights into the behaviors of intrinsically disordered proteins (IDPs) and water. In the first project, local and total solvation thermodynamics around the K-18 domain of the intrinsically disordered protein Tau were compared, and simulated with four pairs of modified and standard force fields. In empirical force fields, an imbalance between intramolecular protein interactions and protein-water interactions often leads to collapsed IDP structures in simulations. To counter this, various methods have been devised to refine protein-water interaction models. This research applied both standard and adapted force fields in simulations, scrutinizing the effects of each adjustment on solvation free energy. In the second project, the MD-based 3D-2PT analysis was utilized to examine variations in local entropy and number density of bulk water in response to an electric field, focusing on the vicinity of reference water molecules. In the third project, various peptide sequences were examined to quantify the free energy involved when specific sequences, known as alpha-MoRFs (alpha-Molecular Recognition Features), transition from intrinsically disordered states to structured secondary motifs like the alpha-helix. The low folding free energy penalty of these sequences can be exploited to design peptide-based or small-molecule drugs. Upon binding to alpha-MoRFs, these drugs can stabilize the helix structure through a binding-induced folding mechanism. Alpha-MoRFs were juxtaposed with entirely disordered sequences from known proteins, with findings benchmarked against leading structure prediction models. Additionally, the binding free energies of various alpha-MoRFs in their folded conformation were assessed to discern if experimental binding free energies reflect the separate contributions of folding and binding, as obtained from umbrella sampling simulations.