Biochips and high-throughput screening methods are powerful tools for studying biological processes. The combination of peptide arrays and SAMDI mass spectrometry incorporates these tools to study a broad range of biochemical transformations, including enzyme activities, to provide valuable information on substrate recognition and guide the development of diagnostic and therapeutic targets. This thesis focuses on the study of two different enzyme classes and modifications to peptide substrates on both a global and local level. The study of omptin proteases illustrates how peptide arrays can reveal optimal peptide substrates with the potential to dramatically improve catalytic efficiency in natural substrates. The study also demonstrates the differences in substrate specificities between two proteases, highlighting the effect of small variations in protein sequence and structure to enzyme activity. The same tools are used to explore epigenetic regulation in oral cancer cell lysates, revealing substrate-specific trends in activity and the class-specific deacetylase enzyme activities that lead to certain cell phenotypes. Finally, genomic biochips are used to analyze global trends in gene expression to compare the extent to which model substrates presenting peptide adhesion motifs mimic the use of conventional cell culture substrates coated with extracellular matrix protein. This work introduces the use of both biochip technologies and self-assembled monolayer surface chemistries to study a broad range of biological processes previously unobservable by standard techniques.

Creator

• Wood, Sarah Elizabeth

DOI

• https://doi.org/10.21985/n2-nw79-0f50

Subject

• Bioengineering

Language

• en

Alternate Identifier

• http://dissertations.umi.com/northwestern:14669
• etdadmin_upload_662973

Keyword

• high-throughput screening
• enzyme activity
• peptides
• self-assembled monolayers
• chemical biology
• biochips

Date created

• 2019-01-01

Resource type

• Dissertation

Rights statement

• In Copyright