Biosynthetic Production and Structural Studies of Glycolipids and Large Fragments of G-Protein Coupled Receptors
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Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2010 Biosynthetic production and structural studies of glycolipids and large fragments of G-protein coupled receptors Kumaran, Sowmini Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-42491 Dissertation Published Version Originally published at: Kumaran, Sowmini. Biosynthetic production and structural studies of glycolipids and large fragments of G-protein coupled receptors. 2010, University of Zurich, Faculty of Science. !" !"&'()'"'()* +,'$" #+0&.+1'*,'$/-02(.$/.")$( 0(12%' /"2".$+0&.( 30-7)+8-079)&'!( 0(172* $)"&(8 ,2/).(9)*)5' *!! :"$$)-$0'" # ;,- ?-20&4,&7(.)-(&0',-="$$)&$'(03$2"*()&(: >$ *=B-.) A:-D($'D(&0'DE D *7)2)4$(.)- E0'()90$"$'(7&0',-="$$)&$'(03$2"*()&(80A,2'F$ .)- I&"F)-$"$F$(HB-"'( D # " !%&'&!()%'('$ 0/$ ,'-&.$! ((((((,- 6 $" #$A 9"$)) ,( -.!2(.!04&5.(!3.(7.!89 (7#89!)'-!:.#8&$;!-.(!2&77.(8'8# $< !,( -.!2(.!= >$!B 4#$7 $ HB-"'(I(LMNM Table of Contents Abbreviation 1 Summary 5 Zusamenfassung 8 Chapter 1 11 1.0 Introduction 11 1.1 Chemistry of protein–carbohydrate interactions 12 1.1.1 Hydrogen bonds 13 1.1.2 Hydrophobic interactions 13 1.1.3 Electrostatic interactions 13 1.1.4 Role of water 14 1.2 Tools for analyzing carbohydrate protein interactions 14 1.2.1 NMR approaches to study carbohydrate–protein Interactions 14 1.2.2 NMR parameters that yield information on protein ligand interactions physiological functions of Y receptors 16 1.2.2.1 Chemical shift 16 1.2.2.2 Relaxation parameters 16 1.2.2.3. NOEs 17 1.2.2.4. Magnetization transfer rates 18 1.2.2.5 Aspects of binding affinity and timescale for detection of NMR parameters 18 1.2.3 Experiments based on chemical shift perturbation 21 1.2.4 Saturation transfer difference (STD) nuclear magnetic resonance experiments to detect ligand binding 21 1.2.5 Water LOGSY: water-ligand observation with gradient spectroscopy 23 1.2.6 Transferred intramolecular nuclear overhauser effects (trNOEs) 23 1.2.6.1 The transferred ROESY experiment 25 1.2.7 Isotope filtering/editing using labeled ligands 25 1.2.8 Spin labeling 27 1.3 Other methods to investigate protein-carbohydrate interactions 28 1.3.1 Molecular dynamics simulations 28 1.3.2 X-Ray crystallography 29 1.3.3 Fluorescence spectrometry in studies of carbohydrate-protein interactions 30 1.3.3.1 Polarisation and anistropy 31 1.3.3.2 FRET 31 1.3.4 Calorimetric experiments 31 1.3.4.1 Isothermal titration calorimetry (ITC) 31 1.3.4.2. Differential scanning calorimetry (DSC) 33 1.3.5 Surface plasmon resonance 33 1.4 Molecules under study 34 1.4.1 Lipopolysaccharides 34 1.4.2 Structure and different types of LPS 35 1.4.3 Structural requirements for the bioactivity of LPS 39 1.4.4 Biosynthesis of LPS 40 1.4.5 LPS signaling pathways 41 1.4.6 Key players of LPS signaling pathway - Endotoxin-binding proteins 43 1.4.6.1 LBP 43 1.4.6.2 BPI 43 1.4.6.3 CD14 44 1.4.6.4 Structure of CD14 45 1.4.6.5 Toll-like receptors 46 1.4.7 LPS responsive cells 47 1.4.7.1 Monocytes 47 1.4.7.2 Polymorphonuclear leukocytes (PMN) 47 1.4.7.3 B- and T-lymphocytes 48 1.4.7.4 Vascular cells, epithelial cells 48 1.4.8 Strategies of endotoxin antagonism 48 1.4.8.1 Anti-endotoxin antibodies 48 1.4.8.2 LPS-binding proteins 49 1.4.8.3 Anti-LPS peptides 49 1.4.8.4 Antimicrobial peptides 49 1.4.9 Polymyxins 50 1.4.9.1 Structure of polymyxins 51 1.4.9.2 Types of polymyxins 51 1.4.9.3 Mechanism of action 53 1.5 Scope of our study 53 1.6 References 55 Chapter 2 2.0 Introduction 62 2.1 A Brief History of GPCRs 63 2.2 GPCR signaling 64 2.3 Significance of GPCRs 66 2.4 Classification of GPCRs 67 2.5 Expression of GPCRs 70 2.6 Current state of structural studies of GPCRs 71 2.6.1 General structure 72 2.6.1.1 Why Seven TMs? 72 2.6.2 The Rhodopsin Structure 73 2.6.2.1 Transmembrane region 74 2.6.2.2 Retinal binding site 75 2.6.2.3 Cytoplasmic surface 76 2.6.2.4 Intramolecular interactions and GPCR activation 76 2.6.3 Opsin/Rhodopsin in the activated state 78 2.6.4 Adrenergic receptors 79 2.6.4.1 !2-adrenergic G-protein coupled receptor 79 2.6.4.2 !1-adrenergic G-protein coupled receptor 81 2.6.4.3 Architecture of the Human A2A Adenosine receptor 82 2.6.5 Comparative analysis of GPCR crystal structures 84 2.7 GPCR oligomerization 87 2.7.1 GPCR studies in fragments 87 2.7.2 Helix –helix interactions 89 2.7.3 A membrane protein folding model 89 2.7.4 Membrane mimetics 90 2.7.4.1 Organic solvents 91 2.7.4.2 Micelles 91 2.7.4.3 Bicelles 92 2.8 Neuropeptide receptors: Aim and scope of the investigation 92 2.9 References 97 Chapter 3 Expression of sCD14 (1-152) in E.coli and Pichia pastoris 104 3.0 Introduction 104 3.1 LPS 104 3.2 CD14 106 3.3 Summary of expression of sCD14(1-152) 107 3.3.1 Recombinant expression of sCD14(1-152) in E.coli 107 3.3.2 Recombinant protein expression in Pichia Pastoris 116 3.3.2.1 The Pichia expression vector 116 3.3.2.2 How it works 117 3.3.2.3 Experimental overview 118 3.3.2.4 Expression of CD14 in Pichia pastoris 118 3.4 Outlook 120 3.5 References 120 Chapter 4 Interactions of lipopolysaccharide and polymyxin studied by NMR spectroscopy 122 4.0 Introduction 122 4.1 Experimental procedures 124 4.1.1 Materials 124 4.1.2 Production of 13C-labelled LPS from the E. coli strain D31m4 124 4.1.3 Production of 13C,15N-labelled PMX-M from P. kobensis M 125 4.1.4 NMR spectroscopy 126 4.1.5 Molecular dynamics calculations 127 4.2 Results 128 4.2.1 Production and purification of 13C-labeled LPS 128 4.2.2 Assignment of LPS and polymyxin resonances 129 4.2.3 Topology of LPS and polymyxin insertion into the DPC micelle 130 4.2.4 Interactions of LPS with various types of polymyxins 131 4.3 Discussions 135 4.4 Acknowledgements 138 4.5 References 138 4.6 Supplementary materials 143 Chapter 5 Studies of the structure of the N-terminal domain from the Y4 receptor, a G-protein coupled receptor and its interaction with hormones from the NPY family 155 5.0 Introduction 155 5.1 Results 157 5.1.1 Recombinant production of N-Y4 157 5.1.2 The structure of N-Y4 158 5.1.3 Topology of membrane-association 161 5.1.4 Immobilizing the N-terminus on the membrane 162 5.1.5 Interaction between N-Y4 and neuropeptides from the NPY family 162 5.2 Discussions 166 5.3 Conclusions 169 5.4 Materials and methods 170 5.4.1 Plasmid construction, expression and purification of N-Y4 171 5.4.2 Synthesis and purification of the neuropeptides and of unlabelled N-terminal fragments 172 5.4.3 Dodecylphosphoethanolamine coupling to carboxyl terminus of N-Y4 173 5.4.4 NMR experiments 173 5.4.5 Membrane-association topology using spin labels 174 5.4.6 Surface plasmon resonance (SPR) studies 174 5.5 Acknowledgement 175 5.6 References 175 5.7 Supplementary materials 177 Chapter 6 Properties of the N-terminal domains from Y receptors probed by NMR spectroscopy 187 6.0 Introduction 187 6.1 Results 190 6.1.1 Expression of N-terminal domains in isotopically-labeled form 190 6.1.2 Assignment of chemical shifts 193 6.1.3 Screening structural properties by 15N relaxation and CD spectroscopy 193 6.1.4 Structures of the N-terminal domains in presence of micelles 195 6.1.5 Interaction studies with neuropeptides from the NPY family 197 6.2 Discussions 200 6.3 Materials and methods 203 6.3.1 Materials 203 6.3.2 Expression and purification of N-terminal domains 203 6.3.3 NMR spectroscopy 205 6.4 Acknowledgements 206 6.5 References 206 6.6 Supplementary materials 211 Chapter 7 Expression of Double Transmembrane Fragments of Y4 Receptor, a Human GPCR, for Structural Studies by NMR Spectroscopy 222 7.0 Introduction 222 7.1 Materials and methods 227 7.1.1 Cloning and mutagenesis to generate double transmembrane constructs of human Y4 receptor into pLC01 vector 227 7.1.2 Protein expression and purification of double transmembrane fragments 229 7.1.3 CNBr cleavage 230 7.1.4 Production of N-His6-3C protease 231 7.1.5 Screening of cleavage conditions for Y4 Trp!LE-TM6-TM7-C by the C3 protease 231 7.1.6 NMR sample preparation 232 7.2 Results and discussion 232 7.2.1 Design and generation of double transmembrane constructs of human Y4- receptor into pLC01 vector 232 7.2.2 The choice of the expression vector systems 233 7.2.3 Selections of E.coli host strains 235 7.2.4 Optimization of inducible expression and purification 237 7.2.5 Optmization of expression in deuterated growth medium 240 7.2.6 Optimization of the cleavage of the fusion protein 241 7.2.7 Detergent screening 245 7.2.8 Construction of larger transmembrane fragments of Y4 receptor 249 7.3 Conclusions 250 7.4 References 252 Curriculum Vitae 254 Acknowledgements 258 Abbreviation AM adrenomedullin AMP Antimicrobial peptide AR adrenergic receptor CARA computer aided resonance assignment CCR2 chemokine C-C motif receptor 2 CCR5 chemokine C-C motif receptor 5 CGRP calcitonin generelated peptide CD circular dichroism CD14 Cluster of differentiation 14 cDNA complementary deoxyriobonucleic acid CHAPS 3-(3-Cholamidopropyl)dimethylammonio)-1-Propanesulfonic Acid CMC critical micelle concentration CNS central nervous system CV column volume CX3C chemokine C-X3-C motif receptor Dab Diamino butyric acid DCM dichloromethane DDM dodecyl-!-d-maltoside DHPC 1,2-Diheptanoyl-sn-Glycero-3-Phosphocholine DIEA diisopropylethylamine DMF dimethyl formamide DPC dodecylphosphocholine Doxyl (4,4-dimethyl-3-oxazolidine-N-oxyl) DTT 1,4-dithiothreitol ECL extracellular loop E.coli Escherichia coli EDTA ethylenediamine tetraacetic acid ELISA enzyme linked immunostaining assay 1 ESI-MS electrospray ionization