Date of Award
12-2018
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Physics and Astronomy
Committee Member
Emil Alexov, Committee Chair
Committee Member
Weiguo Cao
Committee Member
Feng Ding
Committee Member
Hugo Sanabria
Committee Member
Joshua Alper
Abstract
Single nucleotide polymorphism (SNP) is a variation of a single nucleotide in the genome. Some of these variations can cause a change of single amino acid in the corresponding protein, resulting in single amino acid variation (SAV). SAVs can lead to profound alterations of the corresponding biological processes and thus can be associated with many human diseases. This dissertation focuses on integration of existing and development of new computational approaches to model the effects of SAVs with the goal to reveal molecular mechanism of human diseases. Since proton transfer and pKa shifts are frequently attributed to disease causality, the proton transfers in the protein-nucleic acid interactions are investigated and along with development of a new computational approach to predict the SAV’s effect on the protein-DNA binding affinity. The SAVs in four proteins: Lysine-specific demethylase 5C (KDM5C), Spermine Synthase (SpmSyn), 7-Dehydrocholesterol reductase (DHCR7) and methyl CpG binding protein 2 (MeCP2) are extensively studied using numerous computational approaches to reveal molecular details of disease-associated effects. In case of MeCP2 protein, the effects of the most commonly occurring disease-causing mutation, R133C, was targeted by structure-based virtual screening to identify the small molecules potentially to rescue the malfunctioning R133C mutant.
Recommended Citation
Peng, Yunhui, "Modelling the Effects of Disease-Associated Single Amino Acid Variants and Rescuing the Effects by Small Molecules" (2018). All Dissertations. 2269.
https://tigerprints.clemson.edu/all_dissertations/2269