GSBS Dissertations and Theses
Publication Date
2016-05-23
Document Type
Doctoral Dissertation
Academic Program
Biochemistry and Molecular Pharmacology
Department
Biochemistry and Molecular Pharmacology
First Thesis Advisor
Daniel Bolon, PhD
Keywords
Viral Proteins, Genomics, High-Throughput Nucleotide Sequencing, RNA Sequence Analysis, Mutation
Subjects
Dissertations, UMMS; Viral Proteins; Genomics; High-Throughput Nucleotide Sequencing; Sequence Analysis, RNA; Mutation
Abstract
Sequence-function relationship is a fundamental question for many branches of modern biomedical research. It connects the primary sequence of proteins to the function of proteins and fitness of organisms, holding answers for critical questions such as functional consequences of mutations identified in whole genome sequencing and adaptive potential of fast evolving pathogenic viruses and microbes. Many different approaches have been developed to delineate the genotype-phenotype map for different proteins, but are generally limited by their throughput or precision. To systematically quantify the fitness of large numbers of mutations, I modified a novel high throughput mutational scanning approach (EMPIRIC) to investigate the fitness landscape of mutations in important regions of essential proteins from the yeast or RNA viruses. Using EMPIRIC, I analyzed the interplay of the expression level and sequence of Hsp90 on the yeast growth and revealed latent effect of mutations at reduced expression levels of Hsp90. I also examined the functional constraint on the receptor binding site of the Env of Human Immunodeficiency Virus (HIV) and uncovered enhanced receptor binding capacity as a common pathway for adaptation of HIV to laboratory conditions. Moreover, I explored the adaptive potential of neuraminidase (NA) of influenza A virus to a NA inhibitor, oseltamivir, and identified novel oseltamivir resistance mutations with distinct molecular mechanisms. In summary, I applied a high throughput functional genomics approach to map the sequence-function relationship in various systems and examined the evolutionary constraints and adaptive potential of essential proteins ranging from molecular chaperones to drug-targetable viral proteins.
Repository Citation
Jiang, L. Systematic Experimental Determination of Functional Constraints on Proteins and Adaptive Potential of Mutations: A Dissertation. (2016). University of Massachusetts Medical School. GSBS Dissertations and Theses. Paper 854. DOI: 10.13028/M25C74. https://escholarship.umassmed.edu/gsbs_diss/854
DOI
10.13028/M25C74
DOI Link
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