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Chemical Biology-Based Probes for the Labeling of Targets on Live Cells

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Chemical Biology-Based Probes for the Labeling of Targets on Live Cells University of Massachusetts Amherst ScholarWorks@UMass Amherst Doctoral Dissertations Dissertations and Theses November 2015 Chemical Biology-Based Probes For The Labeling Of Targets On Live Cells Amanda M. Hussey University of Massachusetts Amherst Follow this and additional works at: https://scholarworks.umass.edu/dissertations_2 Part of the Biochemistry Commons, Molecular and Cellular Neuroscience Commons, and the Organic Chemistry Commons Recommended Citation Hussey, Amanda M., "Chemical Biology-Based Probes For The Labeling Of Targets On Live Cells" (2015). Doctoral Dissertations. 429. https://doi.org/10.7275/7151287.0 https://scholarworks.umass.edu/dissertations_2/429 This Open Access Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks@UMass Amherst. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. CHEMICAL BIOLOGY-BASED PROBES FOR THE LABELING OF TARGETS ON LIVE CELLS A Dissertation Presented by AMANDA M. HUSSEY Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY September 2015 Department of Chemistry © Copyright by Amanda M. Hussey 2015 All Rights Reserved CHEMICAL BIOLOGY BASED-PROBES FOR THE LABELING OF TARGETS ON LIVE CELLS A Dissertation Presented by AMANDA M. HUSSEY Approved as to style and content by: __________________________________ James J. Chambers, Chair __________________________________ Richard W. Vachet, Member __________________________________ Nathan A. Schnarr, Member __________________________________ Peter Chien, Member __________________________________ Craig T. Martin, Department Head Department of Chemistry DEDICATION To my family and friends. Thank you all. ACKNOWLEDGMENTS I would like to thank my advisor James Chambers for his guidance, patience, and advice over the past six years. To my committee members, Professors Nate Schnarr, Richard Vachet, and Peter Chien, thank you for your advice and insight. I would like to thank Rosie Combs-Bachmann, Nate Johnson, and Dr. Devaiah Vytla for their work on and all of the conversations about nanoprobe 1. I would like to thank Dr. Steve McCarron for his work on nanoprobe 3 and for all the conversations we had. I would also like to thank Adam Gann for his work in synthesizing and testing the photogenerated diazonium probes and for all of the conversations bounce ideas back and forth about nanoprobes. I would also like to thank the other members of the Chambers lab Dr. Kathryne Medeiros and Devon McCarthy and the former members of the Schnarr lab Drs. Gitanjeli Prasad, Jon Amoroso, Lawrence Borketey, and Tsung-Yi Lin for their advice and lively conversation. I would like to thank all the ladies (present and former) in the GWIS peer mentoring group I was in every other Wednesday for most of my Ph.D. Rosie, Angela, Maria, Brittany, Sid, Lisa, Sam, Satamita, Andrea, Debra, and Kate, you have listened and shared so much with me and I am forever grateful. This group was a large part of helping me get through my Ph.D. Thank you. I would like to thank my family for supporting me through this journey. I would like to thank all of my friends that I have made here in the past six years. You guys have been awesome, thank you for the great times and even greater memories. I would finally like to thank my amazing and extremely supportive fiancé Benjamin Johnson. Thank you for reassuring me that I can do this, for listening to all of my complaining, and for being there when I needed you. v ABSTRACT CHEMICAL BIOLOGY-BASED PROBES FOR THE DETECTION OF RECEPTORS ON LIVE CELLS SEPTEMBER 2015 AMANDA M. HUSSEY B.S., UNIVERSITY OF THE SCIENCES IN PHILADELPHIA Ph.D., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor James J. Chambers Proper detection is the key to studying any processes on the cellular scale. Nowhere is this more evident than in the tight space which confines the synaptic cleft. Being able to ascertain the location of receptors on live neurons is fundamental to our understanding of not only how these receptors interact and move inside the cell but also how neurons function. Most detection methods rely on significantly altering the receptor; both tagging with a fluorescent protein or targeting the receptor by a fluorescent reporter in the form of a small molecule causes significant difficulties. These localization techniques often result in forced dimerization, unnatural movement, and at worst inactivation of the receptor. Small molecule organic dyes provide a potential advantage because they can be structurally functionalized to target the protein of interest in a non-perturbing fashion which allows for information to be gathered about the targeted receptor. The work I initiated in the Chambers lab first focused on using a ligand directed fluorophore connected via a photo-labile linker. Through the use of epifluorescence microscopy, I determined that this probe targets glutamate receptors, however questions about subtype inclusion could not be addressed. vi The pharmacophore that our first probe is based on could be much more promiscuous than is presently appreciated in the field of neurobiology. Thus, we designed a new series of probes to allow for covalent modification and affinity purification of endogenous receptors. The second generation of probes set out to answer the questions left by the first. Purified proteins were subjected to SDS-PAGE analysis and could be applied to proteomic identification of receptors. In addition to ligand directed probes, we have also initiated a project on a new, bimolecular photoaffinity probe in which the new methodology continues to develop. The initial studies were performed to ensure that our new strategy is able to be used in biological systems. vii TABLE OF CONENTS Page ACKNOWLEDGMENTS ...................................................................................................v ABSTRACT ....................................................................................................................... vi LIST OF FIGURES…………………………………………………………………………….....xi LIST OF SCHEMES……………………………………………………………………………..xii CHAPTER 1. INTRODUCTION ...........................................................................................................1 1.1 Neuronal Structure ......................................................................................................................................... 1 1.1.2 Synaptic Communication and Plasticity ...................................................................................... 2 1.1.3 Long Term Potentiation..................................................................................................................... 3 1.1.4 Long Term Depression ...................................................................................................................... 5 1.1.5 Glutamate Receptors .......................................................................................................................... 6 1.1.6 Kainate Receptors ............................................................................................................................... 8 1.1.7 NMDARs ............................................................................................................................................... 8 1.1.8 AMPARs ................................................................................................................................................ 9 1.1.9 Calcium Permeability in AMPARs ............................................................................................. 11 1.1.10 Calcium Permeable AMPA Receptors in Excitatory Disease .......................................... 12 1.1.11 Polyamine Toxins as Tools in Neurobiology ......................................................................... 13 1.2 Imaging Techniques .................................................................................................................................... 15 1.2.1 Genetic Imaging Techniques ........................................................................................................ 16 1.2.2 Fluorescent Proteins ........................................................................................................................ 17 1.2.3 Enzymatically Active Tags ........................................................................................................... 17 1.2.4 Small, peptide-based tags .............................................................................................................. 18 1.2.5 Antibodies ........................................................................................................................................... 20 1.2.6 Non-Genetic Imaging Techniques .............................................................................................. 20 1.2.7 Quantum Dots .................................................................................................................................... 21 1.2.8 Ligand-Based Detection ................................................................................................................. 21 1.2.9 Peptide-Based Ligand Delivery .................................................................................................... 22 1.3 Bioorthogonal Chemistry ..........................................................................................................................
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