Date of Award

May 2020

Document Type


Degree Name

Doctor of Philosophy (PhD)


Physics and Astronomy

Committee Member

Emil Alexov

Committee Member

Brian N Dominy

Committee Member

Feng Ding

Committee Member

Joshua Alper


Proteins are involved in many essential roles in the cell including controlling cell dynamics, mobilizing the intracellular response, cell shape etc. A large population of proteins are required to interact with other organelles or other proteins to accomplish their function. Studying protein folding and stability is a great approach to guide the understanding of protein interactions, functions and structures. To implement Gibbs folding free energy of a protein (∆G_folding), the structural information of the native (folded) and unfolded (denatured) state is needed. In this dissertation, we build the ensemble structures for the unfolded state utilizing a random coil model; which is applied to generate the structures for the intrinsically disordered proteins/regions (IDPs/IDRs) as well. These structures are validated using the experimental pKa values of titratable residues. Several studies have shown that the electrostatic interactions between residues in the unfolded structure causes their pKa values to be perturbed in the denatured state compared to those in the native structure. Furthermore, these ensemble structures of the unfolded state are used to calculate Gibbs folding free energy changes of a protein induced by a point mutation (ΔΔG) by implementing Molecular Mechanics Poisson-Boltzmann (MMPBSA) and machine learning (ML) methods. Comparing our estimations with other available servers with this regard, our approach presents quite well predictions employing only physical parameters based on the Gibbs folding free energy change upon a point mutation. Finally, we study the binding of dynein microtubule binding domain (MTBD) and microtubule (MT), specifically by investigating the role of the IDRs in the C-terminal domains of tubulins (called E-hooks and known to be populated with the acidic residues). We show that the transient or dynamic binding occurs between E-hooks and MTBDs, whereas E-hooks exert electrostatic forces on MTBD to provide a “soft-landing” for the MTBD. Furthermore, we indicate the importance of some key residues of MTBD in binding to the MT through the interaction with E-hooks that may provide the essential information for disease studies linked to the mutations in motor proteins.



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