Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)

Legacy Department


Committee Member

Dr. Brian Dominy, Committee Chair

Committee Member

Dr. Dvora Perahia

Committee Member

Dr. Emil Alexov

Committee Member

Dr. Leah Casabianca


In this dissertation, molecular dynamics (MD) simulations were applied to study the effect of single point mutations on protein folding free energy and the protein-ligand binding in the bifunctional protein dihydrofolate reductase-thymidylate synthase (TS-DHFR) in plasmodium falciparum (pf). The main goal of current computational studies is to have a deeper understanding of factors related to protein folding stability and protein-ligand binding. Chapter two aims to seek solutions for improving the accuracy of predicting changes of folding free energy upon single point mutations in proteins. While the importance of conformational sampling was adequately addressed, the diverse dielectric properties of proteins were also taken into consideration in this study. Through developing a three-dielectric-constant model and broadening conformational sampling, a method for predicting the effect of point mutations on protein folding free energy is described, and factors of affecting the prediction accuracy are addressed in this chapter. The following two chapters focus on the binding process and domain-domain interactions in the bifunctional protein pfDHFR-TS. This protein usually plays as the target of antimalarial drugs, but the drug resistance in this protein has caused lots of problems. In chapter three, the mechanism of the development of drug resistance was investigated. This study indicated that the accumulation of mutations in pfDHFR caused obvious changes of conformation and interactions among residues in the binding pocket, which further weakened the binding affinity between pfDHFR and the inhibitor drug. Furthermore, the high rigidity and significantly weakened communications among key residues in the protein binding pocket were exhibited in the pfDHFR quadruple mutant. The rigid binding site was associated with the failure of conformational reorganization upon the binding of pyrimethamine in the quadruple mutant. Chapter four investigated the effect of the N-terminus in pfDHFR-TS on enzyme activity and domain-domain communications. This is the first computational study that focuses on the full-length pfDHFR-TS dimer. This study provided computational evidence to support that remote mutations could disturb the interactions and conformations of the binding site through disrupting dynamic motions in pfDHFR-TS.