Biochemical and structural characterization of chronophin: = Die biochemische und strukturelle Charakterisierung von Chronophin
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| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
Würzburg
November 2014
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| Schlagworte: | |
| Online-Zugang: | kostenfrei Inhaltsverzeichnis |
| Beschreibung: | Veröffentlicht: 2017 |
| Beschreibung: | 161, XIV Blätter Illustrationen, Diagramme |
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| 100 | 1 | |a Knobloch, Gunnar |d 1981- |e Verfasser |0 (DE-588)1125541504 |4 aut | |
| 245 | 1 | 0 | |a Biochemical and structural characterization of chronophin |b = Die biochemische und strukturelle Charakterisierung von Chronophin |c submitted by Gunnar Knobloch from Bogotá, Columbia |
| 246 | 1 | 1 | |a Die biochemische und strukturelle Charakterisierung von Chronophin |
| 264 | 1 | |a Würzburg |c November 2014 | |
| 300 | |a 161, XIV Blätter |b Illustrationen, Diagramme | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a Veröffentlicht: 2017 | ||
| 502 | |b Dissertation |c Julius-Maximilians-Universität Würzburg |d 2015 | ||
| 546 | |a Zusammenfassung in deutscher und englischer Sprache | ||
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| 912 | |a ebook | ||
| 999 | |a oai:aleph.bib-bvb.de:BVB01-029450604 | ||
Datensatz im Suchindex
| _version_ | 1804177055988842496 |
|---|---|
| adam_text | BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION
OF CHRONOPHIN
DIE BIOCHEMISCHE UND STRUKTURELLE CHARAKTERISIERUNG
VON CHRONOPHIN
DISSERTATION FOR A DOCTORAL DEGREE
AT THE GRADUATE SCHOOL OF LIFE SCIENCES,
JULIUS-MAXIMILIAN-UNIVERSITAET WUERZBURG
(SECTION BIOMEDICINE)
SUBMITTED BY
GUNNAR KNOBLOCH
FROM BOGOTA, COLUMBIA
WUERZBURG, NOVEMBER 2014
TABLE O F CONTENTS
A
SUMMARY..........................................................................................................................................V
B
ZUSAMMENFASSUNG................................................................................................................................VII
1
INTRODUCTION.........................................................................................
1
1.1 KINASES AND
PHOSPHATASES....................................................................................................
1
1.2 HALOACID DEHALOGENASE (HAD)
HYDROLASES.......................................................................
6
1.3 THE HAD PHOSPHATASE CH RO N O P H IN
.................................................................................
11
1.4 SUBSTRATES OF C H
RONOPHIN...................................................................................................14
1.4.1 PYRIDOXAL
5 -PHOSPHATE...........................................................................................................
14
1.4.2
COFILIN-1.....................................................................................................................................17
1.4.3
SRC-3.........................................................................................................................................20
1.5 INTERACTION PARTNERS OF C H RO N O P H IN
................................................................................23
1.5.1
SS-ARRESTIN-L..............................................................................................................................23
1.5.2 HEAT-SHOCK PROTEIN
90SS...........................................................................................................23
1.5.3 THE CA2+ AND INTEGRIN BINDING PROTEIN 1
(CIB1).....................................................................24
1.5.4
CALMODULIN................................................................................................................................27
2
MATERIALS............................................................................................
31
2.1 BACTERIAL
STRAINS.....................................................................................................................
31
2.2 M EDIA AND
ANTIBIOTICS..........................................................................................................
31
2.3 ENZYMES AND
PROTEINS..........................................................................................................
32
2.4 A NTIBOD
IES...............................................................................................................................
32
2.5 P RIM
ERS.....................................................................................................................................
32
2.6 PLASM
IDS...................................................................................................................................33
2.7 CHEM
ICALS................................................................................................................................
33
2.8 CRYSTALLIZATION
SCREENS.........................................................................................................35
2.9 E QUIPM
ENT...............................................................................................................................
35
2.10 CONSUM
ABLES..........................................................................................................................
36
2.11 K
ITS.............................................................................................................................................37
2.12 SOFTWARE AND
DATABASES.....................................................................................................
37
3
METHODS..............................................................................................39
3.1 POLYMERASE CHAIN REACTION (PCR)
...................
.
..............................................................
39
3.2 RESTRICTION
DIGESTION.............................................................................................................40
3.3 AGAROSE GEL
ELECTROPHORESIS...............................................................................................41
3.4 GEL E XTRAC TIO N
.........................................................................................................................
41
3.5
LIGATION......................................................................................................................................42
3.6 TRANSFORM ATION OF E. COLI DHSCT FO R M OLECULAR CLO N IN G
............................................
43
3.7 COLONY
PCR..............................................................................................................................
43
3.8 PLASMID P RE P A RA TIO N
.............................................................................................................44
3.9
SEQUENCING..............................................................................................................................
45
3.10 PREPARATION O F CHEMICALLY COM PETENT E.
COLI............................................................... 45
3.11 TRANSFORM ATION OF E. COLI FOR PROTEIN
EXPRESSION........................................................46
3.12 PROTEIN
EXPRESSION................................................................................................................
47
3.13 CELL
LYSIS....................................................................................................................................
47
3.14 PROTEIN
PURIFICATION...............................................................................................................48
3.14.1 IMMOBILIZED METAL ION AFFINITY CHROMATOGRAPHY OF HIS6-TAGGED
PROTEINS
...................
48
3.14.2 ION EXCHANGE
CHROMATOGRAPHY..........................................................................................49
3.14.3 AFFINITY PURIFICATION OF GST-TAGGED PROTEINS
...................................................................
49
3.14.4 HYDROPHOBIC INTERACTION CHROMATOGRAPHY PURIFICATION OF CALMODULIN
........................
50
3.14.5 SIZE EXCLUSION
CHROMATOGRAPHY.........................................................................................51
3.15
UV/VIS-SPECTROSCOPY...........................................................................................................
52
3.16 PAG
E.........................................................................................................................................
52
3.16.1
SDS-PAGE............................................................................................................................
52
3.16.2 TRICINE
SDS-PAGE................................................................................................................
53
3.16.3 PHOS-TAG
SDS-PAGE.............................................................................................................
54
3.17 IM M UNOBLOT/W ESTERN B LO T
................................................................................................
55
3.17.1 STANDARD WESTERN
BLOT.......................................................................................................
55
3.17.2 BLOTTING OF COFILIN-1 SAMPLES SEPARATED BY PHOS-TAG SDS-PAGE
....................................
56
3.18 COOMASSIE BLUE-STAINING OF POLYACRYLAMIDE
GELS........................................................57
3.19 ANALYTICAL U LTRACENTRIFUG
ATION...........................................................................................57
3.20 ANALYTICAL SIZE EXCLUSION C H ROM
ATOGRAPHY...................................................................
58
3.21 T H E RM O FLU O
R...........................................................................................................................
58
3.22
CROSS-LINKING...........................................................................................................................
59
3.23 ISOTHERMAL TITRATION C A LO RIM E TRY
......................................................................................
59
3.24 M ALACHITE GREEN
ASSAY.........................................................................................................60
3.25 PARO-NITROPHENYLPHOSPHATE (PNPP)
ASSAYS..................................................................61
3.26 PHOSPHO-COFILIN-1 DEPHOSPHORYLATION ASSAYS
..............................................................
62
3.27 CIRCULAR DICHROISM (CD)
SPECTROSCOPY............................................................................
63
3.28 PROTEIN
CRYSTALLIZATION..........................................................................................................
63
3.29 DATA
COLLECTION........................................................................................................................
64
3.30 DATA PROCESSING AND
EVALUATION.......................................................................................
65
3.31 M OLECULAR RE P LA C E M E N
T.....................................................................................................67
3.32 M ODEL BUILDING AND RE FIN E M E N
T.......................................................................................
68
4
RESULTS.................................................................................................
69
4.1 PROTEIN
PURIFICATION...............................................................................................................
69
4.1.1 IMMOBILIZED METAL AFFINITY CHROMATOGRAPHY (IMAC)
.........................................................
69
4.1.2 HYDROPHOBIC INTERACTION CHROMATOGRAPHY (HIC) OF CALMODULIN
.......................................
70
4.1.3 ION EXCHANGE CHROMATOGRAPHY OF CHRONOPHINKK
..................................................................
71
4.1.4 AFFINITY CHROMATOGRAPHY OF
GST-CIB1...................................................................................
71
4.1.5 SIZE EXCLUSION
CHROMATOGRAPHY.............................................................................................
72
4.2 CIB1 AND CALMODULIN AS COM PETING INTERACTORS OF
CHRONOPHIN..............................73
4.2.1 CA2+ TRIGGERS COMPLEX FORMATION WITH
CALMODULIN...............................................................
74
4.2.2 THE CHRONOPHIN-CATALYZED PLP HYDROLYSIS IS NOT REGULATED BY CIB1
OR CALMODULIN
........
79
4.2.3 CIB1 AND CALMODULIN HAVE NO EFFECT ON THE CHRONOPHIN MEDIATED
PHOSPHO-COFILIN-1
DEPHOSPHORYLATION..................................................................................................................
81
4.2.4 CIB1 AND CALMODULIN DO NOT INFLUENCE THE PHOSPHOPEPTIDE
PREFERENCES OF
CHRONOPHIN...............................................................................................................................82
4.3 THE ROLE OF CHRONOPHIN D IM E RIZA TIO N
.............................................................................
82
4.3.1 HOMO-OLIGOMERIZATION IS A COMMON FEATURE AMONG HALOACID
DEHALOGENASE
HYDROLASES................................................................................................................................83
4.3.2 GENERATION OF A MONOMERIC CHRONOPHIN VARIANT
.................................................................
84
4.3.3 CHRONOPHINKK IS A MONOMER IN MAMMALIAN CELLS
.................................................................
85
4.3.4 ENZYMATIC CHARACTERIZATION OF MONOMERIC
CHRONOPHIN...................................................... 87
4.3.5 ISOTHERMAL TITRATION CALORIMETRY OF BEF3 BINDING TO CHRONOPHIN^
AND CHRONOPHIN^... 88
4.3.6 STRUCTURAL COMPARISON OF MURINE CHRONOPHINWT AND CHRONOPHIN^
...................................
89
4.3.7 DIMERIZATION AS A POTENTIAL GENERAL MECHANISM REGULATING THE
SPECIFICITY OF C2A-TYPE
HAD
HYDROLASES........................................................................................................................
95
4.4 DETERM INANTS OF SUBSTRATE SPECIFICITIES IN THE C2A-TYPE HAD
HYDROLASES
CHRONOPHIN AND A U M
..........................................................................................................
99
4.4.1 GENERATION OF A HYBRID PROTEIN CONSISTING OF THE CHRONOPHIN
CATALYTIC CORE AND THE
AUM
CAP...................................................................................................................................
99
4.4.2 SUBSTRATE SPECIFICITIES OF CHRONOPHIN, THE CAC HYBRID AND AUM
TOWARDS PLP AND
PNPP........................................................................................................................................101
4.4.3 STRUCTURAL CHARACTERIZATION OF THE CAC
HYBRID....................................................................102
4.5 GENERATION AND CHARACTERIZATION O F CHRONOPHIN-SPECIFIC IN H IB ITO
RS
.................
109
4.5.1 GENERATION OF PUTATIVE CHRONOPHIN-SPECIFIC INHIBITORS
.....................................................
109
4.5.2 BIOCHEMICAL CHARACTERIZATION OF THE
INHIBITORS...................................................................110
4.5.3 STRUCTURAL CHARACTERIZATION OF A CHRONOPHIN-INHIBITOR 3
COMPLEX....................................112
5
DISCUSSION........................................................................................
115
5.1 THE CALCIUM AND INTEGRIN BINDING PROTEIN 1 (CIB1) AND CALMODULIN AS
CHRONOPHIN
INTERACTORS.....................................................................................................
115
5.2 THE ROLE OF CHRONOPHIN D IM ERIZA TIO N
...........................................................................
119
5.3 DETERM INANTS OF SUBSTRATE SPECIFICITIES IN THE C2A-TYPE HAD
HYDROLASES
CHRONOPHIN AND A U M
........................................................................................................124
5.4 GENERATION AND CHARACTERIZATION OF CHRONOPHIN
INHIBITORS..................................130
6
APENDIX............................................................................................136
6.1 SUPPLEM ENTARY D A TA
..........................................................................................................
136
6.1.1 THERMOFLUOR
EXPERIMENTS....................................................................................................
136
6.1.2
CD-SPECTROSCOPY....................................................................................................................
137
6.2 AMINO
ACIDS...........................................................................................................................140
6.3 A
BBREVIATIONS.......................................................................................................................141
6.4
FIGURES.....................................................................................................................................142
6.5
TABLES......................................................................................................................................144
6.6
LITERATURE................................................................................................................................146
C
AFFIDAVIT....................................................................................................................................................
IX
D PUBLICATIONS AND CONFERENCE CONTRIBUTIONS
...........................................................................................
X
E CURRICULUM
VITAE......................................................................................................................................XII
F
ACKNOWLEDGEMENTS...............................................................................................................................XIV
|
| any_adam_object | 1 |
| author | Knobloch, Gunnar 1981- |
| author_GND | (DE-588)1125541504 |
| author_facet | Knobloch, Gunnar 1981- |
| author_role | aut |
| author_sort | Knobloch, Gunnar 1981- |
| author_variant | g k gk |
| building | Verbundindex |
| bvnumber | BV044043609 |
| collection | ebook |
| ctrlnum | (OCoLC)973566959 (DE-599)BVBBV044043609 |
| dewey-full | 610 |
| dewey-hundreds | 600 - Technology (Applied sciences) |
| dewey-ones | 610 - Medicine and health |
| dewey-raw | 610 |
| dewey-search | 610 |
| dewey-sort | 3610 |
| dewey-tens | 610 - Medicine and health |
| discipline | Medizin |
| format | Thesis Book |
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| publishDateSort | 2014 |
| record_format | marc |
| spelling | Knobloch, Gunnar 1981- Verfasser (DE-588)1125541504 aut Biochemical and structural characterization of chronophin = Die biochemische und strukturelle Charakterisierung von Chronophin submitted by Gunnar Knobloch from Bogotá, Columbia Die biochemische und strukturelle Charakterisierung von Chronophin Würzburg November 2014 161, XIV Blätter Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Veröffentlicht: 2017 Dissertation Julius-Maximilians-Universität Würzburg 2015 Zusammenfassung in deutscher und englischer Sprache Pyridoxalphosphat (DE-588)4304162-0 gnd rswk-swf Dimerisierung (DE-588)4251822-2 gnd rswk-swf Inhibitor (DE-588)4027007-5 gnd rswk-swf Phosphatasen (DE-588)4140462-2 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Dimerisierung (DE-588)4251822-2 s Inhibitor (DE-588)4027007-5 s Phosphatasen (DE-588)4140462-2 s Pyridoxalphosphat (DE-588)4304162-0 s DE-604 Erscheint auch als Online-Ausgabe urn:nbn:de:bvb:20-opus-110088 https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-110088 Resolving-System kostenfrei Volltext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029450604&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Knobloch, Gunnar 1981- Biochemical and structural characterization of chronophin = Die biochemische und strukturelle Charakterisierung von Chronophin Pyridoxalphosphat (DE-588)4304162-0 gnd Dimerisierung (DE-588)4251822-2 gnd Inhibitor (DE-588)4027007-5 gnd Phosphatasen (DE-588)4140462-2 gnd |
| subject_GND | (DE-588)4304162-0 (DE-588)4251822-2 (DE-588)4027007-5 (DE-588)4140462-2 (DE-588)4113937-9 |
| title | Biochemical and structural characterization of chronophin = Die biochemische und strukturelle Charakterisierung von Chronophin |
| title_alt | Die biochemische und strukturelle Charakterisierung von Chronophin |
| title_auth | Biochemical and structural characterization of chronophin = Die biochemische und strukturelle Charakterisierung von Chronophin |
| title_exact_search | Biochemical and structural characterization of chronophin = Die biochemische und strukturelle Charakterisierung von Chronophin |
| title_full | Biochemical and structural characterization of chronophin = Die biochemische und strukturelle Charakterisierung von Chronophin submitted by Gunnar Knobloch from Bogotá, Columbia |
| title_fullStr | Biochemical and structural characterization of chronophin = Die biochemische und strukturelle Charakterisierung von Chronophin submitted by Gunnar Knobloch from Bogotá, Columbia |
| title_full_unstemmed | Biochemical and structural characterization of chronophin = Die biochemische und strukturelle Charakterisierung von Chronophin submitted by Gunnar Knobloch from Bogotá, Columbia |
| title_short | Biochemical and structural characterization of chronophin |
| title_sort | biochemical and structural characterization of chronophin die biochemische und strukturelle charakterisierung von chronophin |
| title_sub | = Die biochemische und strukturelle Charakterisierung von Chronophin |
| topic | Pyridoxalphosphat (DE-588)4304162-0 gnd Dimerisierung (DE-588)4251822-2 gnd Inhibitor (DE-588)4027007-5 gnd Phosphatasen (DE-588)4140462-2 gnd |
| topic_facet | Pyridoxalphosphat Dimerisierung Inhibitor Phosphatasen Hochschulschrift |
| url | https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-110088 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029450604&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT knoblochgunnar biochemicalandstructuralcharacterizationofchronophindiebiochemischeundstrukturellecharakterisierungvonchronophin AT knoblochgunnar diebiochemischeundstrukturellecharakterisierungvonchronophin |