Chemical strategies for investigation of deubiquitinases Samuel D. Whedon A dissertation submitted in partial fulfillment of the requirements of the degree of Doctor of Philosophy University of Washington 2018 Reading Committee: Champak Chatterjee, Chair Michael H. Gelb Pradipsinh K. Rathod Program Authorized to Offer Degree: Chemistry © Copyright 2018 Samuel D. Whedon University of Washington Abstract Chemical strategies for investigation of deubiquitinases Samuel D. Whedon Chair of the Supervisory Committee: Dr. Champak Chatterjee Chemistry Regulation of protein structure and function by post-translational modification is a key mechanism in cellular homeostasis. Among known modifications the small protein ubiquitin is unique in the breadth of functions it directs. Regulation of protein ubiquitylation is the function of more than 600 ligases, and ~100 deubiquitinases. Dysregulated ubiquitylation is involved in infection, inflammation, neurodegeneration, metabolic syndromes and cancer. Therapeutic intervention in these conditions benefits from characterization of substrate-specific ligases and deubiquitinases. Substrate specificity is documented among deubiquitinases, but lags behind knowledge of ligases. In the interest of characterizing specificity of cysteine protease deubiquitinases we have developed chemical methods for site-specific ubiquitylation and electrophile incorporation. We began by developing a ubiquitin-derived electrophile through installation of a C-terminal selenocysteine residue, and orthogonal oxidative conversion to dehydroalanine. Upon validation of the electrophile we expanded our substrate scope to a ubiquitylated peptide, with which we i captured the deubiquitinase USP15. In order to access ubiquitylated lysine residues in protein regions inaccessible by native chemical ligation we undertook the synthesis of two selenazolidine amino acids for amber suppression. While conducting amber suppression selections we concurrently pursued semi-synthesis of p53, in order to introduce a C-terminal ubiquitin electrophile. Purification of the semi-synthetic protein proved materially intensive, prompting development of cleavable affinity handles for ligation product purification. A strategy for incorporation at glycine and incorporation at glutamine were developed. A glycine-derived biotin handle proved amenable to reduction by Zn, which furnishes a native glycine, and aromatic thiols, which formed novel site-specific conjugates at the previously modified glycine. Incorporation of a pendant flag tag at glutamine enabled immunoprecipitation followed by traceless tag removal with Zn. ii Acknowledgements I am deeply grateful to the community that has seen me through these past years of study. First and foremost, my family has been a constant inspiration. The kindness, warmth and generosity they show has been my sustenance. I hope to keep their example ever at the front of my mind, along with a reminder to call more often. I thank my friends for their patience and remarkable steadfastness. It is a special caliber of person that meets you after midnight to pass the hours between time points. So too those who often told me simply that they were in town, as I could never commit to plans a week in advance. For the endless outreach (never badgering) to someone so lost in the moment, I am happily indebted. My coworkers have been a daily joy. I have learned so much from all of you, and delighted in your company. The thoughtful collaboration, wise criticism, and resilient good humor have been essential. I count myself lucky to have shared so much of your company. To my mentor, Champak, I owe more than I suspect I fully grasp. Your enthusiasm is infectious, and has carried me through a few bleak patches. Your relentlessness in pursuit of the truth, and challenge to weak arguments, has been instrumental in my development. I am tremendously thankful to have been given so much room to learn through exploration, and I plan to make good use of it. iii Table of Contents Lists of Figures, Schemes, and Tables................................................................................... viii Chapter 1: Introduction to ubiquitylation and protein semi-synthesis................................. 1 1.1 Protein post-translational modifications............................................................................ 1 1.2 Ubiquitin-like modifiers...................................................................................................... 2 1.3 Ubiquitylation & deubiquitylation....................................................................................... 4 1.4 Chemical preparation of homogenously modified proteins............................................... 7 1.5 Chemical preparation of ubiquitin derivatives................................................................. 11 1.6 Purification of semi-synthetic proteins............................................................................ 14 1.7 Aims of this work............................................................................................................ 17 1.8 References..................................................................................................................... 18 Chapter 2: Development of bioorthogonal chemistry for ubiquitin ligation and electrophile incorporation............................................................................................................................. 24 2.1 Introduction..................................................................................................................... 24 2.2 Results and discussion.................................................................................................... 26 2.2.1 Synthesis and reactivity of Ub Gly76Dha N-methylamide................................... 26 2.2.2 Synthesis of SUMO3 Gly92Sec N-methylamide.................................................. 30 2.2.3 Synthesis and reactivity of TRIM25(112-124) K117(UbDha)............................... 32 2.2.4 Synthesis and incorporation of Nε-L-Selenaprolyl-L-Lysine................................. 36 2.2.5 Synthesis and incorporation of (R)-4-[2-[5-selenazolidinyl]acetyl]amino-2- aminobutanoic acid.............................................................................................. 37 2.3 Conclusion and outlook................................................................................................... 40 2.4 Experimental procedures................................................................................................ 41 iv 2.4.1 General methods................................................................................................. 41 2.4.2 Synthesis of (2R,2'R)-3,3'-diselanediylbis(2-amino-N-methylpropanamide)....... 42 2.4.3 Synthesis of (R)-3-(tert-butoxycarbonyl)-1,3-selenazolidine-4-carboxylic acid.... 43 2.4.4 Synthesis of α,α’-di-bromoadipoyl(bis)amide....................................................... 44 2.4.5 Synthesis of Nε-L-Selenaprolyl-L-lysine............................................................... 44 2.4.6 Synthesis of (R)-4-[2-[5-selenazolidinyl]acetyl]amino-2-aminobutanoic acid....... 45 2.4.7 Molecular cloning................................................................................................. 49 2.4.8 Protein overexpression and purification............................................................... 50 2.4.9 Expressed protein ligation of 1 and Ub(1-75) or SUMO3(2-92) α-thioester......... 51 2.4.10 Oxidative conversion of 2 to 3............................................................................. 52 2.4.11 Iodoacetamide alkylation of SUMO3 Gly93Sec N-methylamide.......................... 52 2.4.12 Solid-phase peptide synthesis............................................................................. 52 2.4.13 Expressed protein ligation of TRIM25(112-124) K117(Sec) and Ub(1-75) α- thioester............................................................................................................... 53 2.4.14 Synthesis of 7 from TRIM25(112-124) K117(UbSec) and α,α’-di- bromoadipoyl(bis)amide...................................................................................... 54 2.4.15 General protease labeling.................................................................................... 54 2.4.16 USP15 labeling.................................................................................................... 54 2.4.17 HeLa whole-cell proteome labeling competition assays....................................... 55 2.4.18 BL21ai expression of sfGFP and sfGFP TAG150................................................ 57 2.5 Product characterization and supplemental data............................................................. 58 2.6 References...................................................................................................................... 71 v Chapter 3: Traceless affinity purification handles for the purification of semi-synthetic proteins...................................................................................................................................... 75 3.1 Introduction..................................................................................................................... 75 3.2 Results and discussion.................................................................................................... 78 3.2.1 p53 ligation proof of principle............................................................................... 78 3.2.2 Synthesis