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Mass Spectrometry-Based Global Proteomic Analysis of Endoplasmic Reticulum and Mitochondria Contact Sites

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Mass Spectrometry-Based Global Proteomic Analysis of Endoplasmic Reticulum and Mitochondria Contact Sites Mass Spectrometry-Based Global Proteomic Analysis of Endoplasmic Reticulum and Mitochondria Contact Sites By Chloe N. Poston Bachelor of Science, Clark Atlanta University, Atlanta, GA 2007 Master of Arts, Brown University, Providence, RI 02912 A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in the Department of Chemistry at Brown University Providence, Rhode Island May 2013 © Copyright 2013 by Chloe N. Poston All Rights Reserved ii This dissertation by Chloe N. Poston is accepted in its present form by the Department of Chemistry as satisfying the dissertation requirements for the Degree of Doctor of Philosophy Date Dr. Carthene R. Bazemore-Walker, Director Recommend to the Graduate Council Date Dr. Sarah Delaney, Reader Date Dr. J. William Suggs, Reader Approved by the Graduate Council Date Peter Weber, Dean of the Graduate School iii Curriculum Vitae EDUCATION 2010 Brown University Graduate School, Providence, RI Master of the Arts, Chemistry 2007 Clark Atlanta University, Atlanta, GA Bachelor of Science, Chemistry Provost Scholar PUBLICATIONS C.N. Poston, E. Duong, Y. Cao, C.R. Bazemore-Walker, Proteomic Analysis of Lipid Raft- enriched Membranes Isolated from Internal Organelles, Biochemical and Biophysical Research Communications 415(2) 2011, pg. 355-360. RESEARCH EXPERIENCE Thesis Research: Mass spectrometry based proteomic investigations of internal organelle membranes Accomplishments: Characterized the protein content of lipid enriched detergent resistant membranes found in mitochondria and mitochondria associated membranes Demonstrated the potential influence of detergent resistant membranes in protein and small molecule exchange across internal membranes Identified bona fide mitochondria associated membrane proteins by protein correlation profiling Summer 2007 Brown University Accomplishments: Determined an optimal detergent-free organic based solvent for proteins to be analyzed by ESI LC/MS/MS Summer 2006 University of Pennsylvania Accomplishments: Studied quantum dots to evaluate the frequency and life-time of fluorescence Summer 2005 Georgia Institute of Technology Accomplishments: Optimized a synthetic approach for silica based nanotubes with hydroxy groups tethered to the outer surface Characterized nanotube formation using transmission electron microscopy, X-ray diffraction, and infrared spectroscopy Summer 2004 Skidaway Institute of Oceanography iv Accomplishments: Designed and implemented a waste removal system using aluminosilicate zeolytes Evaluated ammonia concentration, water temperature, and mortality fish daily Created a hydroponic garden using ammonia waste water from fish tanks AWARDS AND RECOGNITION NSF GK-12 Fellowship 2011-2012 ASBMB Travel Award 2011 FASEB MARC Travel Award 2010 Ford Foundation Fellowship Honorable Mention 2008 TEACHING EXPERIENCE AND TRAINING Brown Summer High School, Life Sciences 2011 Methods in Teaching Science Training 2011 Teaching Assistant, Organic Chemistry 2007-2010 ORGANIZATION AFFILIATIONS American Society of Biochemistry and Molecular Biology American Chemical Society Delta Sigma Theta Sorority, Inc v Abstract Mass spectrometry has been a long-standing analytical tool for chemists. Tandem mass spectrometry-based proteomics capitalizes on the sensitivity, accuracy, and efficiency of this classic technique in order to investigate the protein content of specific sub-cellular regions. In this work we apply tandem mass spectrometry (MS/MS) to the analysis of mitochondria-associated endoplasmic reticulum membranes (MAMs). MAMs are a point of communication between the ER and the mitochondria that facilitate Ca2+ trafficking, protein folding, and energy metabolism. They have been implicated in the regulation of apoptosis and more recently neurodegenerative disorders including Alzheimer’s disease and Parkinson’s. The involvement of the MAM in these diseases has yet to be determined, largely because proteins localized to the MAM have yet to be elucidated. We address this gap in knowledge with our tandem mass spectrometry-based global characterization of MAMs from mouse brain tissue. We employ a gel-based LC/LC- MS/MS method that allows for the analysis of hydrophobic membrane proteins. Our analysis reveals 1,212 unique proteins in the MAM that are involved in cell signaling, small molecule trafficking, and protein processing. Bio-informatic analysis of our identified MAM proteins supports postulates that the MAM may play a role in the pathology of Alzheimer’s disease, schizophrenia, and dyskinesia. Our data also suggests that lipid rafts within the MAM are involved in signaling and transport within the region, and may play a role in the MAM’s relationship to neurodegenerative disease. The completion of this work provides a much-anticipated catalog of proteins at the MAM, which can be used for targeted studies to elucidate pathways and novel therapeutic targets in the region. vi Preface and Acknowledgements In 1676, Sir Isaac Newton wrote “if I have seen further, it is by standing on the shoulders of giants”. I, too, contend that I would not have completed this work without the giants in my life who have continuously supported my academic endeavors. I am most grateful to Carthene R. Bazemore-Walker for being a teacher, a mentor, a motivator, and a role model throughout this process. I also wish to acknowledge the members of the Bazemore-Walker group for fostering a collegial and collaborative research environment every single day. I am also appreciative of Professors Sarah Delaney and J. William Suggs for taking time away from their busy schedules to serve as my committee members. Throughout this program, I have been fortunate enough to have the steadfast and unwavering support of my friends and family. They have been the voices of inspiration and positivity that keep me focused. It is my hope that I can one day be a giant that holds up the next generation of scientists, and I dedicate this work to that next generation. vii Table of Contents CHAPTER 1: INTRODUCTION .......................................................................................................................... 1 1.1 Mass Spectrometry-Based Proteomics .................................................................................................. 2 1.1.1 Electrospray Ionization ................................................................................................................... 3 1.1.2 Tandem Mass Spectrometry .......................................................................................................... 4 1.1.3 Computing and Data Processing ..................................................................................................... 5 1.2 Relevant Tandem Mass Spectrometers .................................................................................................. 6 1.2.1 QSTAR Elite .................................................................................................................................. 6 1.2.2 Triple TOF 5600 ............................................................................................................................. 7 1.2.3 Orbitrap Velos ................................................................................................................................ 8 1.3 Mitochondria – Associated Endoplasmic Reticulum Membranes ....................................................... 10 1.3.1 Calcium Trafficking at the MAM ................................................................................................. 11 1.3.2 Structural Linkage Between ER and Mitochondria ...................................................................... 12 1.4 Research Contribution ......................................................................................................................... 13 1.5 Figures ................................................................................................................................................. 14 Figure 1.1: Bottom-up Proteomic Workflow........................................................................................ 14 Figure 1.2: PEPTIDE IDENTIFICATION FROM MASS SPECTRA. ............................................................... 15 Figure 1.3.A: General Schematic of a Quadrupole Time-of-Flight Tandem Mass Spectrometer ........ 16 Figure 1.3.B: General Schematic of an Orbitrap Velos Mass Spectrometer ........................................ 16 Figure 1.4: WIDELY ACCEPTED PROTEINS AND FUNCTIONS IN THE MAM ........................................... 17 1.6 References ........................................................................................................................................... 18 CHAPTER 2: COMPREHENSIVE CHARACTERIZATION OF MITOCHONDRIA-ASSOCIATED ENDOPLASMIC RETICULUM MEMBRANES FROM BRAIN TISSUE ......................................................................................... 22 2.1 Introduction ......................................................................................................................................... 23 2.2 Experimental Procedures ..................................................................................................................... 25 2.2.1 Materials ....................................................................................................................................... 25 2.2.2 MAM Isolation for Mouse Brains ...............................................................................................
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