Graduation Semester and Year
Spring 2026
Language
English
Document Type
Dissertation
Degree Name
Doctor of Philosophy in Chemistry
Department
Chemistry and Biochemistry
First Advisor
Daniel W. Armstrong
Second Advisor
Saiful Chowdhury
Third Advisor
Kevin Schug
Fourth Advisor
Kayunta L. Johnson-Winters
Abstract
N-acyl homoserine lactones (N-HLs) are amino acid derivatives synthesized by gram negative bacteria and act as autoinducer molecules that help in the process of bacterial cell-to-cell communication known as quorum sensing (QS). Through QS bacteria exhibit a collective phenotype that ranges from bioluminescence in Vibrio fischeri to virulence factors in pathogenic bacteria like Pseudomonas aeruginosa and Pectobacterium atrosepcticum. Bacterial QS has been targeted as a way to counter their virulence. Like amino acids, N-HLs possess a chiral center and follow the L/D nomenclature to indicate their stereochemistry. While the process of racemization of N-HLs has not been reported, the presence of D- N-HLs in bacterial samples has sparked recent interest. Studies have revealed biological roles of D-N-HLs in bacteria and as such their detection has become of increasing interest. Like D-AAs, D-N-HLs are usually found in lower concentrations than their L-counterparts, therefore, development of more sensitive and selective techniques are necessary for studying these molecules. Chapter 2 explores the development of extraction methods and analysis through liquid chromatography tandem mass spectrometry (LC-MS/MS) and gas chromatography tandem mass spectrometry (GC-MS/MS) for comprehensive detection of different classes of L/D-N-HLs Chapters 3 and 4 explore the application of methods developed in chapter 2 for detection and quantification of novel L/D-N-HLs in P. aeruginosa and P. atrosepticum.
Amino acids are building blocks of peptides/proteins and changes in their stereochemistry affect overall peptide/protein structure and potentially their function. Epimerization, which is the stereo conversion of a single L-AA to D-AA in peptides, poses challenges in analysis as physical properties of epimers can be similar and their masses are identical. Isomerization in this case refers to conversion of L/D-Asp to L/D-isoAsp, which is a spontaneous change. Chapter 5 explores the use of basic mobile phase additives to improve separation of peptide epimers and isomers. It is shown that switching from acidic to basic additives increases chromatographic resolution for all tested peptide epimers/isomers with the added benefit of higher signal intensity in mass spectrometric detection. Charge state differences between acidic and basic conditions are discussed.
Keywords
Liquid chromatography, mass spectrometry, peptides, epimers, isomers, post-translational modifications, N-acyl homoserine lactones
Disciplines
Analytical Chemistry
License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Recommended Citation
Dhaubhadel, Umang, "Isomerization of Amino Acids and Amino Acid Derivatives: Consequences on Post-translational Modifications and Analysis Methods" (2026). Chemistry & Biochemistry Dissertations. 1.
https://mavmatrix.uta.edu/chemistry_dissertations2/1