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Structural and Functional Analyses of the Interaction of Tetherin with the Dendritic Cell Receptor ILT7 Nicolas Aschman

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Structural and Functional Analyses of the Interaction of Tetherin with the Dendritic Cell Receptor ILT7 Nicolas Aschman Structural and functional analyses of the interaction of tetherin with the dendritic cell receptor ILT7 Nicolas Aschman To cite this version: Nicolas Aschman. Structural and functional analyses of the interaction of tetherin with the dendritic cell receptor ILT7. Biomolecules [q-bio.BM]. Université Grenoble Alpes, 2015. English. NNT : 2015GREAV064. tel-01682995 HAL Id: tel-01682995 https://tel.archives-ouvertes.fr/tel-01682995 Submitted on 12 Jan 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. #$ !"#$% '!"(%")!*+%"+% %&'$()*%$*+,(-./$)#.0*%$*2)$-&3+$ ,-.0'*('$."1"34565748*#9:;<9;:=68*89*-=>5?4565748 2!!3$."5'&'6$.!'%("1"7"*8$"9::; !.6% $.%"-*! -4<56=@*A#'BA- <=>6%"+'!').%"-*!"(%"C:"D4>E:48F*D$.##$-&)- -!.-*!.%"* "6%' "+%"( (>49*5E*/4:; *5 9*'866*.>98:=<945> +* 6"6G0<568*%5<95:=68*'(4I48*89*#<48><8 *F;*/4J=>9 A>=6K 8 * 9:;<9;:8668 *89* E5><945>>8668 *F8*6,4>9,:=<945>* F8*6=*9,9(8:4>8*=J8<*68*:,<8N98;: .+. <=>6%"6 $% %"- #('A %5% $"(%*P0*=J:46*P12TB +%C* $"(%"D !E"05-6."+%"1" %:*A>F:8=*'.BA)$++. FG*--!$% !( %:*4J8 *2A(%.- FG*--!$% !( C:*B=:<*5AB.- F!.6'+% $( %:*A>F:86*B<'A)4 FIJ*5' *$% !( %:*+=;:8>9*$))A%& FIJ*5' *$% !( C:*D4>E:48F*D$.##$-&)- FK%5#!%( !"#$ % ()*$"+,(-*.# "#(/( !"#$ %&(0 "##"(1"23$(-#56"(/( !"#$ % (7%"2,58(/( !"#$ %&(2"(75!* "(/(9#"*:8"(;<0( Structural and functional analysis of the interaction of tetherin with the dendritic cell receptor ILT7 Nicolas Aschman June 28, 2015 ii Abstract Human immunodeficiency virus 1 (HIV-1) specifically infects CD4+ T cells, thereby preventing an appropriate activation of cytotoxic T cells and B cells in response to opportunistic pathogens. In addition, HIV-1 antagonises host restriction factors, in- cluding tetherin. In the absence of the viral protein Vpu, tetherin potently inhibits virus particle release from infected cells. Tetherin also triggers proinflammatory sig- naling upon sensing virus assembly, and activates the dendritic cell receptor ILT7. The principal objective of this thesis was to elucidate the structural details underlying the interaction of tetherin with ILT7. Despite difficulties in the production of recombinant ILT7, the crystal structure of the N-terminal ILT7 domain could be determined. Fur- thermore, binding of tetherin to full-length ILT7, but not to the N-terminal domain, could be confirmed by SPR. These results provide a solid basis for the more detailed characterisation of the interaction. Résumé Le virus d’immunodéficience humaine 1 (VIH-1) cible spécifiquement les cellules CD4+ et empêche ainsi l’activation de cellules T cytotoxiques et B lors d’une infection sec- ondaire. Le VIH-1 antagonise également la plupart des facteurs de restriction de l’hôte, y compris la tétherine. En l’absence de la protéine virale Vpu, la tétherine inhibe le re- larguage de particules virales et provoque leur dégradation. La tétherine est également capable d’induire une signalisation pro-inflammatoire en réponse au bourgeonnement viral ainsi que d’activer le récepteur de cellules dendritiques ILT7. L’objectif princi- pal de cette étude consistait à élucider les bases structurales de l’interaction entre la tétherine et ILT7. Malgré de nombreuses difficultés rencontrées dans la production re- combinante de ILT7, on a pu déterminer la structure cristallographique du domaine N-terminale du récepteur. La ligation de la tétherine à l’ectodomaine entier de ILT7, mais pas au domaine N-terminal, a également été montré. Ces résultats constituent une base solide pour la caractérisation plus détaillée de l’interaction. iii iv Acknowledgements First and foremost, I would like to express my gratitude to my supervisor Winfried Weissenhorn for giving me the chance of joining his team at a time when my back- ground in structural biology was limited to a few rusty memories from early morning lectures. When my project turned out to be more challenging than expected and ini- tially had me seriously struggling, Winfried has always remained supportive and con- fident. Among many other things, I greatly appreciate that the door of Winfried’s office was always open, that he always took time for discussion and was always available for advice. I would like to thank the members of my jury, namely Andrea Cimarelli and Yves Gaudin, who act as rapporteurs, as well as Marc Jamin, Andrew McCarthy and Laurent Terradot. I am very grateful also to Carlo Petosa and Ramesh Pillai for their construc- tive feedback as members of my thesis advisory committee. During the last year of my thesis I have been involved in a fruitful collaboration with the laboratory of Prof Eric Cohen (Institut de Recherches Cliniques de Montréal, Canada). In this regard, I would especially like to thank Mariana Bego for sharing her insights and providing protein samples, as well as Edouard Côté for analysing my samples by flow cytometry. I am indebted to all of my team members for teaching me virtually everything about protein expression, purification and crystallography. I am especially thankful to Patricia Renesto for introducing me to the art of cloning, for sharing her experience of mammalian cell culture, for co-writing my first review article and generally for her helpfulness. I will miss her anecdotes and always remember the good moments shared in the lab. Special thanks also go to Miriam Hock for teaching me many techniques and helping me troubleshoot my experiments countless times ; to Jens Radzimanowski for introducing me to protein crystallisation, X-ray diffraction and data processing ; to Christophe Caillat for his help with model building and refinement, and generally use- ful advice ; and to Aurélien Dordor for untold scientific and less-scientific discussions. I will also fondly remember my colleagues Pauline Macheboeuf, Géraldine Mayeux and Nolwenn Miguet, as well as previous team members David Lutje Hulsik, Nicolas Martinelli and Emilie Poudevigne. Many other people have been helpful by teaching me new techniques or providing useful advice, among them Pascal Fender whom I would like to thank for his help with cell culture and SPR, as well as for his eternal good mood and humour ; Vladimir Rybin and Piotr Gerlach for introducing me to ITC and MST analysis, respectively ; Sergiy Avilov for his help with confocal microscopy and Natasha Alexandrovna for her advice on protein expression in mammalian cell lines. Filip Yabukarski has helped me, through countless discussions, make light of some of the more obscure aspects of protein crystallography. I am also thankful to Nicolas Tarbouriech, Max Nanao and v Chloe Zubieta for their spontaneous advice on crystallographic data processing and model refinement. In the context of the Partnership for Structural Biology (PSB, Grenoble), I have made use of several platforms and facilities, most notably the Eukaryotic Expression Facility (EEF) operated by the Berger group where all insect cell expression was carried out. I am grateful to the Berger team for providing this service, with special thanks to Alice Aubert for always providing me with healthy cells at a moment’s notice. I would also like to thank Philippe Mas (thermal shift assays), Daphna Fenel and Guy Schoehn (electron microscopy) and Luca Signor (mass spectrometry). The administrative and technical staff of my host laboratory have been extremely helpful and kind, and I would like to thank Sandrine Vignon in particular for her assis- tance with awkward paperwork of all kind. I would like to acknowledge the financial support of the Agence Nationale de la Recherche sur le SIDA et les hépatites virales (ANRS) and the Fonds National de la Recherche of Luxembourg (FNR). Last but not least I would like to thank my parents for their unconditional support in all my endeavours, and my wife Corinne for her undying optimism, patience and love. Nick Aschman Grenoble, March 2015 vi Contents Abstract......................................... iii Acknowledgements.................................. v Abbreviations ..................................... xi Introduction (français) 15 1 Introduction 17 1.1 Molecular and structural biology of HIV . ..... 19 1.1.1 Assemblyandbudding . 20 1.1.2 Infectionandreplication. 22 1.2 InnateimmuneresponsetoHIV . 26 1.2.1 Interferonresponse.. .. .. .. .. .. .. .. 27 1.2.2 Restrictionfactors. 29 1.3 Tetherinstructureandfunction . .... 31 1.3.1 Expressionandtrafficking. 32 1.3.2 Topologyandstructure . 33 1.3.3 Inhibitionofvirusrelease . 35 1.3.4 Organisation of subcellular structure . ..... 41 1.3.5 Immunesensingandsignalingactivities . ... 42 1.3.6 Modulationoftheinnateimmuneresponse . .. 42 1.4 ILT7 and the leukocyte Ig-like receptor family . ........ 43 1.4.1 Topology, structure and signal transduction . ...... 44 1.4.2 Functional activity and role in HIV-1 infection . ...... 45 Objectives 51 2 Methods 53 2.1 Bioinformatics.................................. 53 2.1.1 Multiple sequence alignment and phylogenetics . ..... 53 2.1.2 Domain, structure and disorder prediction . .... 54 2.1.3 Post-translational modifications and processing . ....... 54 2.1.4 Ab initio protein–protein docking and interface characterisation . 54
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