Chaperonin-catalyzed rescue of kinetically trapped states in protein folding [Elektronische Ressource] / Jyoti Sinha

Sinha Jyoti

Informations

• Publié par: ludwig-maximilians-universitat_munchen
• Publié le: 01 janvier 2010
• Nombre de lectures: 21
• Langue: English
• Poids de l'ouvrage: 7 Mo

Extrait

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


Chaperonin-Catalyzed Rescue of Kinetically
Trapped States in Protein Folding

Jyoti Sinha

aus
Patna
Bihar/India

2010
Erklärung
Diese Dissertation wurde im Sinne von § 13 Abs. 3 bzw. 4 der Promotionsordnung vom 29.
Januar 1998 (in der Fassung der vierten Änderungssatzung vom 26. November 2004) von
Herrn Prof. Dr. F. Ulrich Hartl betreut





Ehrenwörtliche Versicherung

Diese Dissertation wurde selbständig, ohne unerlaubte Hilfe erarbeitet.


München, den












Dissertation eingereicht am 18.11.2010
1. Gutacher Dr. F. Ulrich Hartl
2. Gutachter PD. Dr. Konstanze Winklhofer
Mündliche Prüfung am 14.12.2010  Acknowledgements
I am grateful to Dr. Manajit Hayer-Hartl and Prof. Dr. F. Ulrich Hartl for giving me the
opportunity to learn and interact with some of the best minds. I would like to take this
opportunity to thank them for their encouragement, faith, continual support and giving me the
freedom to learn from my mistakes. Their ideas and advice have been crucial for
development of this project and me as a person.
I would like to thank PD. Dr. Konstanze Winklhofer for being a co-referee of my thesis and
my thesis advisory committee members Prof. Dr. Dr. Walter Neupert and Prof. Dr. Alexander
Buchberger.
I would also like to thank our very competent and helpful support system Andrea, Silke and
Evelyn who were always there with kind words and solutions to all my administrative and
other problems making my stay in Munich smooth.
I am also grateful to Elisabeth, Bernd, Dirk, Nadine, and Emmanuel for all their logistical
support and help. I am indebted to all my colleagues in the department of cellular
biochemistry and specially office A-1 for making the working and learning a pleasurable
experience. In particular, help and suggestions provided by Alex Hastie has been valuable to
my learning curve.
I sincerely thank Dr. Yun-Chi Tang for her enthusiasm in mentoring me during initial phases
of my PhD and Eva and Romy for their excellent technical assistance.
This work essentially is a result of the team work together with Manal and Kausik, with
whom I have learned more about scientific temper than just technicalities. Many thanks to
Bernhard Poschner, Guoxin Jiang and Martin Sikor for helpful suggestions during the course
of this work.
My heartfelt thanks to the ‘Bhartiye Junta’ here Pratibha, Shruti, Bhumi, Juhi, Pankaj, Partho
Rashmi, Sathish, Madhu, Anoop, Ranga, Naga, Kirti, Rochelle, Aarathi, Krishna, Venky, Niti
and Rajat for endless parties and all the fun.
My deepest thanks to Vivek for his enormous support in this journey. And at last, what
actually stands first is the unconditional love and encouragement of my parents and brothers
(Deepak and Prakash) whose unwavering belief in me made it all happen. CONTENTS i 
 
1. Summary ............................................................................................................ 1 
2. Introduction ...................................................................................... 3 
2.1. Protein Folding ............................................................................................................ 3 
2.1.1. Protein Structure ................................................................... 3 
2.1.2. Dominant Forces in Protein Folding ............................................................ 6 
2.1.3. Mechanism of Protein Folding .........................7 
2.1.4. Classical View versus New View to Protein Folding Kinetics .................... 8 
2.1.5 Disulfide Bonds Mediated Protein Folding ................................................ 16 
2.2. Methods for Studying Protein Folding ..................................................................... 17 
2.2.1. Fluorescence ..............................19 
2.2.2. FRET .......................................................................................................... 21 
2.2.3. Single Molecule FRET ......................................24 
2.3. Protein Folding In Vivo ............................................................................................. 26 
2.3.1. The Chaperone Network in the Cytosol ....................................30 
2.3.2. Ribosome-Associated Chaperone : Trigger Factor .................................... 32 
2.3.3 The Bacterial Hsp70 System .....................................................34 
2.3.4. The Chaperonins ................................................................. 36 
2.4 Group I Chaperonin System: GroEL and GroES ..................................................... 37 
2.4.1 Architecture of GroEL and GroES ............................................37 
2.4.2. Polypeptide, Nucleotide and GroES Binding ............................................. 40 
2.4.3. Mechanism of GroEL/ES mediated Protein Folding .................................. 44 
2.4.4. Substrates of GroEL .................................................................48 
3. Aim of the Study .............................................................................................. 49 
4. Materials and Methods ................................................................................... 50 
4.1. Materials ................................................................................................................. 50 
4.1.1. Chemicals ................................................................................................... 50 
4.1.2 Enzymes .............53 
4.1.3. Materials ............................................................................. 53 
4.1.4. Instruments ......................................................................... 53 
4.1.5. Media .................................................................55 
4.1.6. Antibotic Stock Solutions ........................... 55 
4.2. Bacterial Strains and Plasmids ................................................................................. 55 
4.2.1. E.coli strains .............................................................................55 
4.2.2. Plasmids .............................................................................. 55 
4.3. Molecular Cloning Methods ..........................................58 

 CONTENTS ii

4.3.1. Preparation and Transformation of E. coli Competent Cells ...................... 58
4.3.2. Plasmid Purification ................................................................................... 59
4.3.3. PCR Amplification ..................... 59
4.3.4. DNA Restriction and Ligation .................................................................... 60
4.3.5. DNA Analytical Methods ........... 61
4.4. Protein Purification ................................... 61
4.4.1. GroEL Expression and Purification ............................................................ 61
4.4.2. GroES Expression and Purification 62
4.4.3. MBP and MBP Mutants Expression and Purification ................................ 63
4.4.4. MetF Expression and Purification .............................................................. 64
4.4.5. Rhodanese Preparation ............................................................................... 64
4.5. Protein Analytical Methods ..................... 65
4.5.1. Determination of Protein Concentration 65
4.5.2. SDS-PAGE ................................................................................................. 65
4.5.3. Western-Blotting ........................ 66
4.6. GroEL Functional Activity Assays ........................................................................... 67
4.6.1. ATPase Assay ............................................................. 67
4.6.2. Aggregation Prevention Assay of Denatured Rhodanese ........................... 67
4.7. In vitro Protein Refolding and Activity Assays ....................................................... 68
4.7.1. MBP Refolding ................................ 68
4.7.2. MetF Refolding ........................... 69
4.7.3. Rhodanese Refolding .................................................. 69
4.7.4. Rubisco Refolding ...................................................... 70
4.8. Biochemical and Biophysical Methods .................................................................. 71
4.8.1. Thiol-Mediated Labeling of the Cys Constructs ........ 71
4.8.2. Characterization of Cysteine Pair Mutants of DM-MBP ........................... 71
4.8.3. D