Development of MAS solid state NMR methods for structural and dynamical characterization of biomolecules [Elektronische Ressource] / Veniamin Shevelkov. Gutachter: Klaus Peter Hofmann ; Bernd Reif ; Andreas Herrmann

Veniamin Shevelkov

Sujets

• Biologie

Informations

• Publié par: humboldt-universitat_zu_berlin
• Publié le: 01 janvier 2011
• Nombre de lectures: 16
• Langue: English
• Poids de l'ouvrage: 8 Mo

Extrait

Development of MAS solid state NMR methods for
structural and dynamical characterization of
biomolecules
Dissertation
zur Erlangung des akademischen Grades
doctor rerum naturalium
(Dr. rer. nat.)
im Fach Biophysik

eingereicht an der
Mathematisch-Naturwissenschaftlichen Fakultät I
der Humboldt-Universität zu Berlin

von
Herrn Veniamin Shevelkov


Präsident der Humboldt-Universität zu Berlin
Prof. Dr. Christoph Markschies

Dekan der Mathematisch-Naturwissenschaftlichen Fakultät I
Prof. Dr. Christian Limberg

Gutachter:
1. Prof. Dr. Klaus Peter Hofmann
2. Prof. Dr. Bernd Reif
3. Prof. Dr. Andreas Herrmann

Tag der mündlichen Prüfung: 22. April 2008
Contents.

Acknowledgements..................................................................................6
List of publications:................................................................................8
Abbreviations: ......................................................................................10
1 Chapter. General Introduction......................................................11
1.1 Structural and dynamical investigations of biological systems by
solid-state NMR spectroscopy. .................................................................................... 11
1.2 Distances and angles in proteins and peptides................................... 12
1.3 The dynamics of a quantum mechanical systems.............................. 16
1.4 Density operator. .................................................................................. 18
1.5 The nuclear spin and NMR spectroscopy. ......................................... 18
1.6 Spin one half in a static field................................................................ 20
1.7 Operator algebra. ................................................................................. 20
1.8 The nuclear spin Hamiltonian in the static field. .............................. 22
1.9 Spherical representation of the spin Hamiltonian............................. 24
1.10 Reference frames and magic angle spinning in solid state NMR..... 25
1.11 Interaction frame.................................................................................. 27
1.12 Average Hamiltonian theory. .............................................................. 29
1.13 Basic solid state NMR techniques. ...................................................... 29
1.14 Overview of the thesis. ......................................................................... 36
2 Chapter. Proton detection in MAS solid state NMR of proteins. ..38
3
2.1 Introduction. ......................................................................................... 38
2.2 Sample preparation and NMR spectroscopy..................................... 40
1
2.3 H Detection in MAS ssNMR spectroscopy of proteins employing
Pulsed Field Gradients for residual solvent suppression.......................................... 40
2.4 Ultra-high resolution in proton solid-state NMR at high levels of
deuteration. 44
2.5 Conclusion............................................................................................. 51
3 Chapter. Transverse relaxation optimized spectroscopy in MAS
solid-state NMR of proteins. ...........................................................................52
3.1 Introduction. ......................................................................................... 52
3.2 Experimental section............................................................................ 54
3.3 Experimental results. ........................................................................... 56
4 Chapter. Quantitative analysis of backbone dynamics in
microcrystalline sample of the SH3 domain of α-spectrin by MAS solid-state
NMR. .......................................................................................................72
4.1 Introduction. ......................................................................................... 72
4.2 Experimental section............................................................................ 73
4.3 Theoretical background....................................................................... 78
4.4 Experimental results. ........................................................................... 81
4.5 Simulated results and discussions....................................................... 95
5 Chapter. Detection of water molecules in a microcrystalline
sample of the SH3 domain of α-spectrin by MAS solid-state NMR. ............105
5.1 Introduction. ....................................................................................... 105
5.2 Materials and solid state NMR methods. ......................................... 107
4
5.3 Results.................................................................................................. 108
5.4 Discussion............................................................................................ 114
6 Chapter. Resolution enhancement in MAS solid-state NMR by
13application of C homonuclear scalar decoupling during acquisition. ......124
6.1 Introduction. ....................................................................................... 124
6.2 Experimental....................................................................................... 126
6.3 Results and discussion........................................................................ 128
References: ........................................................................................136
15Appendix 1.1. Simulation of N peaks ratio. .....................................155
15Appendix 2.1. Simulation of N line width. .......................................158
Appendix 2.2 Experimental values for T ,, T and η for SH3. ...........160 1 2
15 1Appendix 2.3 SIMPSON input file to extract N- H dipolar coupling
values. ...........................................................................................................165
15 1Appendix 2.4. Fitting results for N- H dipolar coupling values......167
Appendix 2.5 C++ code to fit correlation parameters. .....................169
Appendix 2.6. Simulated results for motional parameters.................175
Summary .............................................................................................178
Zusammenfassung...............................................................................180
5

Acknowledgements.


This research work was carried out under supervision of Prof. Dr. Bernd Reif at
Department Chemie, Technische Universität München, from March 2002 to March 2003
and at the Leibniz-Institut für Molekulare Pharmakologie (FMP-Berlin) from April 2003
to June 2007. I would like to express my deepest gratitude to the people who supported
and helped me during my doctoral research.
Firstly, I would like to thank my supervisor Prof. Dr. Bernd Reif. For his
encouragement and support, which were invaluable all the time. His scientific guidance
and fruitful ideas were base for my successful research work. Numerous interesting and
stimulating discussions formed my scientific views and were a key point for my results.
His trust and concerns on me allowed to keep my own scientific freedom and opinion. I
thank him for excellent scientific environment and perfect working conditions.
A special thanks to Dr. Anne Diehl and Kristina Rehbein for preparing all SH3
samples used in my work. Without this collaboration many results of my research would
not be possible.
Thanks to Prof. Dr. Horst Kessler for the perfect NMR facilities in München.
I am grateful to Prof. Dr. Hartmut Oschkinat for the state of art NMR facilities and
for good scientific cooperation.
Thanks to Dr. Barth Jan van Rossum for help and guidance in struggling with
NMR hardware problems, for scientific cooperation, helpful discussions and cheerful
mood.
I thank Dr. Frank Eisenmenger for time and efforts he spend for tutorial and help
in respect of computer’s soft- and hardware.
Thanks to all former and current members of Bernd’s group, for your help, support
and just nice time. Jing and Sarav were persons who made friendly atmosphere in the
group where I came. Thanks Maggy, Vipin, Juan Miguel and Rasmus also for solid state
NMR discussions. My officemates Tomas and Rasmus for pleasant working and personal
6
atmosphere. Thanks to Murali, Mangesh, Katja, Uwe, Po and Stefan for good and
interesting contacts.
I am also thankful for people in Hartmut’s group, especially in solid state NMR
division. I have to single out Stefan Jehle for scientific contacts.

Veniamin Shevelkov, Berlin June 2007.
7
List of publications:


This thesis is based on the following papers and reviews:

1. Chevelkov V., Rossum B.J.v., Castellani F., Rehbein K., Diehl A., Hohwy M.,
Steuernagel S., Engelke F., Oschkinat H. and Reif B., H-1 detection in MAS solid-
state NMR Spectroscopy of biomacromolecules employing pulsed field gradients
for residual solvent suppression. Journal of the American Chemical Society (2003)
Vol 125, pp 7788-7789.
2. Chevelkov V., Faelber K., Diehl A., Heinemann U., Oschkinat H.