Electronic Thesis and Dissertation Repository

Thesis Format

Integrated Article


Master of Science




Shawn Li


Post-translational modifications (PTM) are vital regulators of protein function and homeostasis. The role of dynamic regulations of non-histone lysine methylated proteins (NHKMP) recently began to be recognized in DNA damage repair, apoptosis and transcriptional pathways. My goal was to identify components of the NHKMP network to understand its importance in a healthy versus diseased cellular state. I used membrane peptide arrays to systematically characterize nine naturally occurring lysine methyl binding domains (KMBD). Five KMBDs were chosen based on their overlapping specificities to achieve maximum coverage of lysine methylated peptides. These five KMBDs was used to enrich for methylated lysine peptides from a trypsinized HEK293 cell lysate and followed by mass spectrometry identification. We identified 229 NHKMP and 301 novel sites from HEK293. The amount of NHKMPs and sites that I have identified in total was unprecedented: this allows us to gain valuable insights into components of the lysine methylome network.

Summary for Lay Audience

Proteins can have many modifications post-synthesis, called post-translational modification. These PTMs are responsible for regulating vital pathways within the cells and ensure the survival of the cells. In this thesis, I studied one type of PTM called protein lysine methylation. Protein lysine methylations are found in DNA regulation, cell regulation and other pathways. It is also widespread to have dysregulation of protein lysine methylation within cancer cells. To understand how protein lysine methylation works within the cell, we first need to identify the proteins that are methylated. Current methods cannot identify a vast range of methylated lysine proteins within one experiment. Therefore, for my thesis, I developed a method to enrich and identify methylated lysine proteins. In this thesis, I was able to identify several novel proteins that were methylated within the cell.

Included in

Biochemistry Commons