Structural and biochemical analysis of the UvrA binding module of the bacterial transcription repair coupling factor Mfd [Elektronische Ressource] / Nora Aßenmacher

Nora Aßenmacher

Sujets

• Biologie

Informations

• Publié par: ludwig-maximilians-universitat_munchen
• Publié le: 01 janvier 2006
• Nombre de lectures: 15
• Langue: English
• Poids de l'ouvrage: 2 Mo

Extrait

Dissertation zur Erlangung des Doktorgrades
der Fakultät für Chemie und Pharmazie
der Ludwig-Maximilians-Universität München



Structural and biochemical analysis of the
UvrA-binding module of the bacterial
transcription-repair coupling factor Mfd





Nora Aßenmacher

aus

Paderborn




München, 2006 Erklärung
Diese Dissertation wurde im Sinne von § 13 Abs. 3 bzw. 4 der Promotionsordnung vom
29. Januar 1998 von Herrn Prof. Dr. Karl-Peter Hopfner betreut.






Ehrenwörtliche Versicherung
Diese Dissertation wurde selbständig, ohne unerlaubte Hilfe erarbeitet.

München, am 09.10.2006



....................................................
(Nora Aßenmacher)











Dissertation eingereicht am 09.10.2006
1. Gutachter Herr Prof. Dr. Karl-Peter Hopfner
2. Gutachter Herr Prof. Dr. Patrick Cramer
Mündliche Prüfung am 18.12.2006 The presented thesis was prepared in the time from June 2002 to June 2006 in the
laboratory of Professor Dr. Karl-Peter Hopfner at the Gene Center of the Ludwig-
Maximilians-University of Munich (LMU).



















Parts of this PhD thesis have been published:


Assenmacher, N. and Hopfner K.-P. (2004).
MRE11/RAD50/NBS1: complex activities (Review). Chromosoma 113(4):
157-166.


Assenmacher, N., Wenig, K., Lammens, A. and Hopfner, K.-P. (2006).
Structural basis for transcription coupled repair: the N-terminus of Mfd resembles
UvrB with degenerate ATPase motifs. Journal of Molecular Biology 355(4):
675-683.




























"[One] topic we touched on was mutation ... We totally missed the possible role of …
[DNA] repair although … I later came to realise that DNA is so precious that probably
many distinct repair mechanisms would exist. Nowadays, one could hardly discuss
mutation without considering repair.”
Francis Crick in "The double helix: a personal view" (Crick, 1974). Table ofcontents
Table of contents
1 INTRODUCTION .......................................................................................................................................1
1.1 DNA REPAIR .........................................................................................................................................1
1.1.1 Nucleotide excision repair .......................................................................................................2
1.1.1.1 NER in bacteria .................................................................................................................................. 3
1.1.1.2 Comparison of NER in eukaryotes to the bacterial system ............................................................... 5
1.1.2 Transcription-coupled DNA repair..........................................................................................5
1.1.2.1 Transcriptional arrest and rescue........................................................................................................ 6
1.1.2.2 The Mfd protein is the bacterial transcription-repair coupling factor ............................................... 6
1.1.2.3 Domain architecture and biochemical properties of Mfd .................................................................. 8
1.1.2.4 UvrA binding.................................................................................................................................... 10
1.1.2.5 Eukaryotic TCR................................................................................................................................ 11
1.2 STRUCTURE DETERMINATION BY X-RAY CRYSTALLOGRAPHY.......................................................... 12
1.2.1 Structural biology.................................................................................................................. 12
1.2.2 Structure determination by X-ray crystallography............................................................... 13
1.2.2.1 Theory of X-ray diffraction.............................................................................................................. 13
1.2.2.2 Structure factors and electron density .............................................................................................. 14
1.2.2.3 Phasing by use of anomalous dispersion..........................................................................................15
1.3 OBJECTIVES........................................................................................................................................ 18
2 MATERIALS AND METHODS............................................................................................................. 20
2.1 MATERIALS........................................................................................................................................ 20
2.2 MOLECULAR BIOLOGY METHODS ...................................................................................................... 20
2.2.1 Cloning .................................................................................................................................. 20
2.2.2 Site-directed mutagenesis...................................................................................................... 21
2.3 MICROBIOLOGY METHODS................................................................................................................. 23
2.3.1 Transformation of E.coli ....................................................................................................... 24
2.3.2 Protein expression................................................................................................................. 25
2.3.3 Selenomethionine-labelling................................................................................................... 25
2.4 PROTEINCHEMICAL METHODS............................................................................................................ 27
2.4.1 Protein purification ............................................................................................................... 27
2.4.2 Protein-protein interaction assay ......................................................................................... 28
2.5 PROTEIN ANALYSIS ............................................................................................................................ 29
2.5.1 Analytical size exclusion chromatography ........................................................................... 29
2.5.2 Limited proteolysis ................................................................................................................ 29
2.5.3 Denaturing polyacrylamide gel electrophoresis (SDS-PAGE)............................................ 30
2.5.4 Protein sequencing (Edman, 1950)....................................................................................... 30
2.5.5 Matrix assisted laser desorption ionisation Time-of-Flight analysis .................................. 30

Table ofcontents
2.6 FUNCTIONAL ASSAYS......................................................................................................................... 31
2.6.1 ATPase activity assay............................................................................................................ 31
2.6.2 DNA binding assay................................................................................................................ 32
2.7 STRUCTURAL ANALYSIS OF MFD-N2................................................................................................. 33
2.7.1 Protein crystallization by sitting drop vapour diffusion....................................................... 33
2.7.2 Crystallization of Mfd-N2...................................................................................................... 35
2.7.3 Data collection, structure determination, model building and refinement.......................... 35
3 RESULTS .................................................................................................................................................. 37
3.1 FULL-LENGTH E.COLI MFD................................................................................................................ 37
3.1.1 Purification and crystallization of full-length Mfd............................................................... 37
3.1.2 Limited proteolysis ................................................................................................................ 38
3.2 PURIFICATION, CRYSTALLIZATION AND STRUCTURE DETERMINATION OF MFD-N2 ......................... 41
3.2.1 Purification of Mfd-N2 ..........................................................................................................41
3.2.2 Crystallization ....................................................................................................................... 42
3.2.3 Data collection .................