Spectroscopical investigations to determine RNA-ligand interactions and RNA dynamics [Elektronische Ressource] / von Jan Ferner

Jan

Informations

• Publié par: goethe_universitat_frankfurt_am_main
• Publié le: 01 janvier 2009
• Nombre de lectures: 9
• Langue: English
• Poids de l'ouvrage: 6 Mo

Extrait

Spectroscopical Investigations to
Determine RNA-Ligand
Interactions and RNA Dynamics

Dissertation
Zur Erlangung des Doktorgrades
der Naturwissenschaften

vorgelegt beim Fachbereich Biochemie, Chemie und Pharmazie der
Goethe-Universität
in Frankfurt am Main

von
Jan Ferner
aus New Rochelle, USA

Frankfurt 2009
vom Fachbereich Biochemie, Chemie und Pharmazie der Goethe-Universität
Frankfurt als Dissertation angenommen.

Dekan: Prof. Dr. D. Steinhilber

Gutachter: Dr. Harald J. Schwalbe
Prof. Michael Göbel

Datum der Disputation: 2009Für meine Eltern und meine Frau Elke This thesis was prepared under the supervision of Prof. Dr. Harald J.
Schwalbe between November 2002 and July 2009 at the Institute for Organic
Chemistry and Chemical Biology of the Goethe-University Frankfurt am Main.
TABLE OF CONTENTS
TABLE OF CONTENTS
CHAPTER I
SUMMARY & OVERVIEW............................................................. 1
List of Publications .................................................................. 4
CHAPTER II
RNA BIOMACROMOLECULES ....................................................... 7
RNA - History and Functions 7
RNA – Structure and Dynamics ..................................................12
Primary Structure ...................................................................12
Secondary Structure ...............................................................13
Double Helices ................................................................13
Hairpin Loops..................................................................16
Internal Loops.................................................................18
Bulges............................................................................19
Tertiary Structure...................................................................20
Dynamics ..............................................................................21
I TABLE OF CONTENTS
CHAPTER III
RNA TARGETS & LIGANDS ........................................................27
The Human Immunodeficiency Virus (HIV)................................28
Packaging Signal Element Ψ.....................................................29
Tryptophane-Rich Peptide Ligands of HIV Ψ-RNA.................31
Transactivation Response Element TAR .....................................32
Arginine-Flanked Synthetic Peptide Ligands of HIV TAR-RNA .34
The Coxsackievirus B3 ...............................................................36
Stemloop D Subdomain of the Cloverleaf RNA ............................36
CHAPTER IV CHAPTER IV
NMR THEORY & METHODOLOGIES..............................................39
Ligand Binding Interactions.......................................................39
Resonance Assignment ..............................................................42
RNA......................................................................................42
Peptide Ligand .......................................................................53
Structure Determination of RNA-Ligand Complexes...................55
Determination of Structural Restraints.......................................55
Hydrogen-Bond Distance Restraints....................................55
NOE Distance Restraints ...................................................57
Dihedral Restraints ..........................................................58
Orientational Restraints....................................................60
II TABLE OF CONTENTS
Structure Calculation...............................................................62
ARIA..............................................................................63
HADDOCK.......................................................................64
Determination of global and local dynamics ..............................66
Autocorrelated Relaxation........................................................66
Longitudinal Relaxation ....................................................66
Transverse Relaxation ......................................................67
Longitudinal Relaxation in a Rotating Frame........................69
Sources of Spin Relaxation.......................................................69
Relaxation of a Spin S in an I-S Spin System..............................71
Derivation of Dynamical Information from Autocorrelated Relaxation
Rates....................................................................................73
Global Dynamics..............................................................73
Local Dynamics ...............................................................74
CHAPTER V
THE Ψ-RNA HEXAPEPTIDE LIGAND
Research Article: Identification of Peptide Ligands for Target RNA
Structures Derived from the HIV-1 Packaging Signal Ψ by Screening
Phage-Displayed Peptide Libraries ...................................................81
Research Article: A Tryptophan-Rich Hexapeptide Inhibits Nucleic Acid
Destabilization Chaperoned by the HIV-1 Nucleocapsid Protein............89
III TABLE OF CONTENTS
Research Article: Inhibition of HIV-1 by a Peptide Ligand of the
Genomic RNA Packaging Signal Ψ..................................................105
CHAPTER VI
STRUCTURE OF A TAR RNA-LIGAND COMPLEX
Research Article: Tripeptides from Synthetic Amino Acids Block the
Tat-TAR Association and Slow Down HIV Spread in Cell Cultures .......119
Research Article: Structures of HIV TAR RNA-Ligand Complexes Reveal
Higher Binding Stoichiometries......................................................129
CHAPTER VII
FAST DYNAMICS IN RNA TETRALOOPS
Research Article: Quantitative Γ-HCNCH: Determination of the
Glycosidic Torsion Angle χ in RNA Oligonucleotides from the Analysis of
CH Dipolar Cross-Correlated Relaxation by Solution NMR Spectroscopy
.................................................................................................147
Research Article: NMR and MD Studies of the Temperature-Dependent
Dynamics of RNA YNMG-Tetraloops................................................173

IV TABLE OF CONTENTS
GERMAN SUMMARY
SPEKTROSKOPISCHE UNTERSUCHUNGEN ZUR BESTIMMUNG VON RNA-
LIGAND WECHSELWIRKUNGEN UND RNA DYNAMIKEN...................203
REFERENCES
..........................................................................................209
CURRICULUM VITAE
.227
ACKNOWLEDGEMENT
..........................................................................................230

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