Chemical tools for the study of proteolytic activities associated with
antigen presentation
Swieten, Paul Franciscus van
Citation
Swieten, P. F. van. (2007, January 18). Chemical tools for the study of proteolytic activities
associated with antigen presentation. Retrieved from https://hdl.handle.net/1887/9143
Version: Corrected Publisher’s Version
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CHEMICAL TOOLS FOR THE STUDY OF
PROTEOLYTIC ACTIVITIES ASSOCIATED
WITH ANTIGEN PRESENTATION
Cover design and printing:
Optima Grafische Communicatie, Rotterdam
CHEMICAL TOOLS FOR THE STUDY OF
PROTEOLYTIC ACTIVITIES ASSOCIATED
WITH ANTIGEN PRESENTATION
PROEFSCHRIFT
TER VERKRIJGING VAN
DE GRAAD VAN DOCTOR AAN DE UNIVERSITEIT LEIDEN,
OP GEZAG VAN RECTOR MAGNIFICUS DR. D. D. BREIMER,
HOOGLERAAR IN DE FACULTEIT DER WISKUNDE EN
NATUURWETENSCHAPPEN EN DIE DER GENEESKUNDE,
VOLGENS BESLUIT VAN HET COLLEGE VOOR PROMOTIES
TE VERDEDIGEN OP DONDERDAG 18 JANUARI 2007
KLOKKE 16.15 UUR
DOOR
PAUL FRANCISCUS VAN SWIETEN
GEBOREN TE DE LIER IN 1977
Samenstelling promotiecommissie
Promotores : Prof. dr. H. S. Overkleeft
Prof. dr. G. A. van der Marel
Referent : Dr. J. W. Drijfhout
Overige leden : Prof. dr. J. J. C. Neefjes
Dr. B. M. Kessler (University of Oxford)
Dr. H. Ovaa
Prof. dr. J. Brouwer
6
Table of contents
List of abbreviations 8
General introduction 11
Chapter 1 Bioorthogonal chemistry in living cells:
novel strategies for labeling biomolecules 17
Chapter 2 Detection of active proteasomes by a two-
step labeling strategy 35
Chapter 3 A cell permeable inhibitor and activity
based probe for the caspase-like activity of
the proteasome 45
Chapter 4 Development of an isotope-coded activity
based probe for the quantitative profiling of
cysteine proteases 59
Chapter 5 A cysteine protease probe with an
additional amine-reactive group 75
Table of Contents
7
Chapter 6 A cell penetrating cysteine protease probe 83
Summary and future prospects 95
Samenvatting 99
List of publications 103
Curriculum vitae 105
Nawoord 107
8
List of abbreviations 1
ABP activity based probe Ac acetyl
Ada 1-adamantyl acetyl Ahx 6-amino-hexanoic acid amc 7-amino-4-methyl coumarin Aoh 7-amino-3-oxaheptanoic acid aq. aqueous
Bn benzyl
Boc tert-butyl-oxycarbonyl br s broad singlet
Cat cathepsin cv column volume d doublet
DAPI 4',6-diamidino-2-phenylindole DCG Doron C. Greenbaum
dd doublet of doublets
DIC diisopropyl carbodiimide DiPEA N,N-diisopropyl ethylamine DMAP 4-dimethylaminopyridine DMF N,N-dimethylformamide DMSO dimethylsulfoxide DNA deoxyribonucleic acid DTT dithiothreitol
E. coli Escherichia coli
EDC 1-ethyl-3-(3-dimethylaminopropyl)- carbodiimide
EDTA ethylene diamine tetraacetic acid ESI-MS electrospray ionization mass spectrometry Et ethyl
eq. molar equivalent FALI fluorophore-assisted laser inactivation
FCS fetal calf serum
Fmoc 9-fluorenylmethyloxycarbonyl FRET fluorescence resonance energy transfer
GlcNAc N-acetyl-D-glucosamine GFP green fluorescent protein
GM-CSF granulocyte macrophage-colony stimulating factor GST glutathione S-transferase hAGT human O(6)-alkylguanine-DNA alkyltransferase HATU N-[(Dimethylamino)-1H-1,2,3-tri- azolo[4,5-b]pyridine-1-lmethylene]-
N-methylmethanaminium hexa- fluorophosphate HCTU N-[(1H-6-Chlorobenzotriazolo-1- yl)(dimethylamino)methylene]-N- methylmethanaminium hexafluorphosphate N-oxide HIV human immunodeficiency virus HOBt 1-hydroxybenzotriazole HPLC high performance liquid chromatography HRMS high resolution mass spectrometry HRP horseradish peroxidase ICAT isotope coded affinity tag JPM Joseph P. Meara
LC/MS liquid chromatography/mass spectrometry LPS lipopolysaccharide m multiplet
List of Abbreviations
7 HMPB 4-(4-hydroxymethyl-3-methoxy-
phenoxy)butyryl Me methyl
MHC major histocompatibility complex Mtt 4-methyl-triphenylmethyl Nle, nL norleucine
NMP N-methyl-2-pyrrolidone
NMR nuclear magnetic resonance OVA ovalbumin
PAGE polyacrylamide gel electrophoresis Pbf 2,2,4,6,7-pentamethyldihydrobenzo- furan-5-sulfonyl PBMC peripheral blood mononuclear cell PBS phosphate buffered saline
Pmc 2,2,5,7,8-pentamethylchroman-6- sulfonyl
ppm parts per million PVDF polyvinyl difluoride PyBOP (benzotriazol-1-yloxy)-
tripyrrolidino-phosphonium hexafluorophosphate q quartet
RNA ribonucleic acid RP reverse phase
RPMI Roswell Park Memorial Institute rt retention time s singlet
sat. saturated
SDS sodium dodecyl sulfate SPPS solid phase peptide synthesis Strept streptavidine
Su succinimidyl Suc succinyl t triplet tBu tert butyl TES triethyl silane
Tf trifluoromethylsulfonyl TFA trifluoro acetic acid
THF tetrahydrofuran TIS triisopropyl silane TLC thin layer chromatography TMEDA N,N,N',N'-tetramethylene ethylenediamine TMS tetramethyl silane Tr triphenylmethyl tRNA transfer ribonucleic acid Ts 4-tolylsulfonyl UV ultraviolet
1. 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.
