Chemical tools to probe the proteasome
Verdoes, M.
Citation
Verdoes, M. (2008, December 19). Chemical tools to probe the proteasome. Retrieved from https://hdl.handle.net/1887/13370
Version: Corrected Publisher’s Version
License: Licence agreement concerning inclusion of doctoral thesis in the Institutional Repository of the University of Leiden
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Chemical Tools To Probe The Proteasome
PROEFSCHRIFT
ter verkrijging van
de graad van Doctor aan de Universiteit Leiden,
op gezag van Rector Magnificus prof.mr. P.F. van der Heijden, volgens besluit van het College voor Promoties
te verdedigen op vrijdag 19 december 2008 klokke 13.30 uur
door
Martijn Verdoes
geboren te Leiden in 1980
Promotiecommissie
Promotores : Prof. dr. H. S. Overkleeft : Prof. dr. G. A. van der Marel
Overige leden : Prof.dr. J. Brouwer
Prof.dr. J.J. Neefjes
Prof.dr. J. Lugtenburg
Dr. B. M. Kessler
As long as we’re having fun...
List of Abbreviations
Chapter 1
General Introduction
Chapter 2
A Fluorescent Broad-Spectrum Proteasome Inhibitor for Labeling Proteasomes In Vitro and In Vivo.
Chapter 3
Acetylene functionalized BODIPY dyes and their application in the synthesis of activity based proteasome probes.
Chapter 4
Azido-BODIPY acid: a new tool in activity-based protein profiling
Chapter 5
Mixing of peptides and electrophilic traps gives rise to potent, broad- spectrum proteasome inhibitors.
6 9
31
51
63
83
Table of contents
Chapter 6
Synthesis and evaluation of subunit specific proteasome probes.
Chapter 7
Diels-Alder two-step activity-based proteasome labeling
Chapter 8
Summary and Future Prospects
Samenvatting
List of Publications
Curriculum Vitae
Nawoord
101
127
139
153
156
158
159
6 ABP Activity-based probe
ABPP Activity-based protein profiling
Ac acetyl
AcCl acetyl chloride Ac2O acetic anhydride AcOH acetic acid Ada 1-adamantyl acetyl Ahx 6-aminohexanoic acid AMC 7-acetoxy-4-methyl-coumarin AMP adenosine monophosphate APT attached proton test
ATP adenosine triphosphate aq. aqueous
NA naphthylamide Bax Bcl-2-associated X protein Bio biotin
BM biotinylated molecular marker Boc tert-butyloxycarbonyl
Boc2O tert-butyloxycarbonic anhydride BODIPY boron-dipyrromethene,
boradiazaindacene
BOP benzotriazol-1-yl-oxy-tris- (dimethylamino)phosphonium hexafluorophosphonate BSA bovine serum albumine
Bu butyl
calcd. calculated
cat. catalytic amount CDI carbodiimidazole
CLSM confocal laser scanning microscopy CtL chymotrypsin-like
chemical shift d doublet
Da Dalton
DABCO 1,4-diazabicyclo[2.2.2]octane
DBU diazabicyclo[5.4.0]undec-7-ene DC dual color marker
DCE 1,2-dichloroethane DCM dichloromethane dd double doublet
ddd double double doublet DIC differential interference contrast
List of Abbreviations
7 DIC N,N’-diisopropyl carbodiimide
DIFO difluorinated cyclooctyne DiPEA Diisopropylethylamine
DMAP 4-(dimethylamino)pyridine DMEM dulbecco's modified eagle's medium DMF N,N-dimethylformamide
DMSO dimethylsulfoxide dt double triplet
DTNB 5,5’-dithio-bis(2-nitrobenzoic acid) DTT dithiothreitol
DUB deubiquitinating enzyme
dq double quartet
EDC·HCl 1-ethyl-3-(3-dimethyl-aminopropyl)- carbodiimide HCl salt
EDTA ethylenediaminetetraacetate EL-4 murine lymphoid cell line
Et3N triethyl amine Et2O diethyl ether EtOH ethanol EtOAc ethyl acetate equiv. molar equivalent ES ethyl methyl sulfone FDA United States food and drug
administration
Fmoc (9H-fluoren-9-yl)methoxycarbonyl GFP green fluorescent protein
HCTU (2-(6-Chloro-1H-benzotriazole- 1-yl)- 1,1,3,3-tetramethylaminium
hexafluorophosphate)
HEK293T human embryonic kidney cell line HeLa human cervix carcinoma cell line HEPES 4-(2-hydroxyethyl)-1-
piperazineethanesulfonic acid HMB 3-hydroxy-2-methylbenzamide
HMPB 4-hydroxymethylphenyl-butyric acid linker
HOBt N-hydroxybenzotriazole HOSu N-hydroxysuccinimide hr. hour(s)
HRMS high resolution mass spectrometry
Hz Hertz
i.v. intravenous IFN- interferon-gamma IB inhibitor of NF-B J coupling constant K kelvin
LC/MS liquid chromatography/ mass spectrometry
LiHMDS lithium hexamethyldisilazide m multiplet
M molar
M molecular marker MBHA p-methylbenzhydryl amine
Me methyl
MeCN acetonitrile
MelJuSo metastasizing human melanoma cell line
MeOD CD3OD MeOH methanol
MES 2-(N-morpholino)ethane sulfonic acid min. minute(s)
nBu n-butyl
NEM N-ethyl maleimide
MS (ESI) mass spectrometry (electrospray ionization)
NF-B nuclear factor-B NIP nitro-iodophenol MHC I major histocompatibility
complex class I NMM N-methylmorpholine NMP N-methyl-2-pyrrolidone NMR nuclear magnetic resonance
8 Ntn N-terminal nucleophilic
m/z mass-to-charge ratio o/n overnight
OAc acetate
PBS phosphate buffered saline Pd/C palladium on charcoal PEG polyethyleneglycol PetEt petroleum ether
PGPH peptidylglutamyl peptide hydrolytic
Ph phenyl
ppm parts per million pv. pathovar
PyBOP benzotriazol-1-yl-oxy-tripyrrolidino- phosphonium
hexafluorophosphonate q quartet
quant. quantitative
RAW Mouse leukaemic monocyte macrophage cell line
RPMI roswell park memorial institute medium
rt room temperature Rt retention time s singlet
sacc. Pier Andrea Saccardo sat. saturated
SDS-PAGE sodium dodecyl sulfate-poly acrylamide gel electroforese sp. species
Su succinimidyl t triplet t, tert tertiary
T temperature
TAP transporter associated with antigen presentation
TBAI tetrabutylammonium iodide
TBS tert-butyldimethylsilyl tBu tert-butyl
tBuONO tert-butyl nitrite tBuOH tert-butanol td triple doublet TEA triethyl amine TFA trifluoroacetic acid THF tetrahydrofuran TIS triisopropyl silane TL trypsin-like
TLC thin layer chromatography TMR tetramethylrhodamine TMS trimethylsilyl
Tol. toluene
Tris 2-amino-2-(hydroxymethyl)-1,3- propanediol
SDS sodium dodecyl sulphate SPPS solid phase peptide synthesis Su succinimidyl
Ub ubiquitin
UPS Ubiquitin Proteasome System
VE vinyl ethyl ester
VO(acac)2 vanadium(IV)acetyl acetonate VS vinyl methyl sulfone
Z benzyloxycarbonyl
Note: the one and three letter codes for the amino acids follow the recommendations of IUPAC. J. Biol.
Chem. 1968, 243, 3557-3559 and J. Biol. Chem. 1972, 247, 977-983.
