Advertisement

Solid-State NMR Investigations of the MHC II Transmembrane Domains: Topological Equilibria and Lipid Interactions

  • Christopher Aisenbrey
  • Evgeniy S. Salnikov
  • Burkhard BechingerEmail author
Article
  • 44 Downloads
Part of the following topical collections:
  1. Membrane and Receptor Dynamics

Abstract

The major histocompatibility complex class II (MHC II) membrane proteins are key players in the adaptive immune response. An aberrant function of these molecules is associated with a large number of autoimmune diseases such as diabetes type I and chronic inflammatory diseases. The MHC class II is assembled from DQ alpha 1 and DQ beta 1 which come together as a heterodimer through GXXXG-mediated protein–protein interactions and a highly specific protein-sphingomyelin-C18 interaction motif located on DQA1. This association can have important consequences in regulating the function of these membrane proteins. Here, we investigated the structure and topology of the DQA1 and DQB1 transmembrane helical domains by CD-, oriented 2H and 15N solid-state NMR spectroscopies. The spectra at peptide-to-lipid ratios of 0.5 to 2 mol% are indicative of a topological equilibrium involving a helix crossing the membrane with a tilt angle of about 20° and another transmembrane topology with around 30° tilt. The latter is probably representing a dimer. Furthermore, at the lowest peptide-to-lipid ratio, a third polypeptide population becomes obvious. Interestingly, the DQB1 and to a lesser extent the DQA1 transmembrane helical domains exhibit a strong fatty acyl chain disordering effect on the inner segments of the 2H-labelled palmitoyl chain of POPC bilayers. This phosphatidylcholine disordering requires the presence of sphingomyelin-C18 suggesting that the ensemble of transmembrane polypeptide and sphingolipid exerts positive curvature strain.

Keywords

Transmembrane dimer Highly specific protein–lipid interaction Supported lipid bilayer Solid-state NMR Helix topology Fatty acyl chain order parameter 

Abbreviations

DHPC

1,2-Dihexanoyl-sn-glycero-3-phosphocholine

DMPC

1,2-Dimyristoyl-sn-glycero-3-phosphocholine

DQA1-TMD

KK TETVV CALGL SVGLV GIVVG TVFII RGLRS KK

DQB1-TMD

KK QSKML SGIGG FVLGL IFLGL GLIIH HRSQK K

LWHH

Line width at half height

MHC

Major histocompatibility complex

NMR

Nuclear magnetic resonance

POPC

1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

SM

Sphingomyelin

SM-C18

N-octadecanoyl-d-erythro-sphingosylphosphorylcholine

TMD

Transmembrane domain

Notes

Acknowledgements

The discussions with Britta Brügger and Thomas Kupke on p24, MHC II and in particular DQA1 and its specific interactions with sphingomyelin are gratefully acknowledged. We thank Arnaud Marquette for his help with first CD spectra.

Author Contributions

ES and CA designed and performed the experiments and analysed data, BB helped in the design the experiments and in the analysis and wrote the paper.

Funding

We are grateful for the financial contributions of the Agence Nationale de la Recherche (Projects ProLipIn 10-BLAN-731, membraneDNP 12-BSV5-0012, MemPepSyn 14-CE34-0001-01, InMembrane 15-CE11-0017-01 and the LabEx Chemistry of Complex Systems 10-LABX-0026_CSC), the University of Strasbourg, the CNRS, the Région Alsace and the RTRA International Center of Frontier Research in Chemistry. BB thanks the Institut Universitaire de France for support and for providing additional time for research.

Compliance with Ethical Standards

Conflict of interest

All authors declare that they have no conflict of interest.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

232_2019_71_MOESM1_ESM.docx (9.5 mb)
Supplementary material 1 (DOCX 9733 kb)

References

  1. Aisenbrey C, Bechinger B (2004) Tilt and rotational pitch angles of membrane-inserted polypeptides from combined 15N and 2H solid-state NMR spectroscopy. Biochemistry 43:10502–10512CrossRefGoogle Scholar
  2. Aisenbrey C, Sizun C, Koch J, Herget M, Abele U, Bechinger B, Tampe R (2006) Structure and dynamics of membrane-associated ICP47, a viral inhibitor of the MHC I antigen-processing machinery. J Biol Chem 281:30365–30372CrossRefGoogle Scholar
  3. Aisenbrey C, Sudheendra US, Ridley H, Bertani P, Marquette A, Nedelkina S, Lakey JH, Bechinger B (2007) Helix orientations in membrane-associated Bcl-XL determined by 15N solid-state NMR spectroscopy. Eur Biophys J 37:71–80CrossRefGoogle Scholar
  4. Aisenbrey C, Marquette A, Bechinger B (2019a) The mechanisms of action of cationic antimicrobial peptides refined by novel concepts from biophysical investigations (Chap. 4). In: Matsuzaki K (ed) Antimicrobial peptides, advances in experimental medicine and biology. Springer, Singapore, pp 33–64CrossRefGoogle Scholar
  5. Aisenbrey C, Kemayo-Koumkoua P, Salnikov ES, Glattard E, Bechinger B (2019b) Investigations of the structure, topology, and interactions of the transmembrane domain of the lipid-sorting protein p24 being highly selective for sphingomyelin-C18. Biochemistry.  https://doi.org/10.1021/acs.biochem.9b00375 Google Scholar
  6. Anderson HA, Roche PA (2015) MHC class II association with lipid rafts on the antigen presenting cell surface. Biochim Biophys Acta 1853:775–780CrossRefGoogle Scholar
  7. Batchelder LS, Niu H, Torchia DA (1983) Methyl reorientation in polycrystalline amino acids and peptides: a 2H NMR spin lattice relaxation study. J Am Chem Soc 105:2228–2231CrossRefGoogle Scholar
  8. Bechinger B (2001) Membrane insertion and orientation of polyalanine peptides: a 15N solid-state NMR spectroscopy investigation. Biophys J 82:2251–2256CrossRefGoogle Scholar
  9. Bechinger B (2009) Rationalizing the membrane interactions of cationic amphipathic antimicrobial peptides by their molecular shape. Curr Opin Colloid Interface Sci Surf 14:349–355CrossRefGoogle Scholar
  10. Bechinger B, Opella SJ (1991) Flat-coil probe for NMR spectroscopy of oriented membrane samples. J Magn Reson 95:585–588Google Scholar
  11. Bechinger B, Salnikov ES (2012) The membrane interactions of antimicrobial peptides revealed by solid-state NMR spectroscopy. Chem Phys Lipids 165:282–301CrossRefGoogle Scholar
  12. Bechinger B, Sizun C (2003) Alignment and structural analysis of membrane polypeptides by 15N and 31P solid-state NMR spectroscopy. Concepts Magn Reson 18A:130–145CrossRefGoogle Scholar
  13. Bechinger B, Resende JM, Aisenbrey C (2011) The structural and topological analysis of membrane-associated polypeptides by oriented solid-state NMR spectroscopy: established concepts and novel developments. Biophys Chem 153:115–125CrossRefGoogle Scholar
  14. Bertani P, Raya J, Bechinger B (2014) 15N chemical shift referencing in solid state NMR. Solid-State NMR Spectrosc 61–62:15–18CrossRefGoogle Scholar
  15. Bethune J, Kol M, Hoffmann J, Reckmann I, Brügger B, Wieland F (2006) Coatomer, the coat protein of COPI transport vesicles, discriminates endoplasmic reticulum residents from p24 proteins. Mol Cell Biol 26:8011–8021CrossRefGoogle Scholar
  16. Bjorkholm P, Ernst AM, Hacke M, Wieland F, Brugger B, von Heijne G (2014) Identification of novel sphingolipid-binding motifs in mammalian membrane proteins. Biochim Biophys Acta 1838:2066–2070CrossRefGoogle Scholar
  17. Contreras FX, Ernst AM, Haberkant P, Björkholm P, Lindahl E, Gönen B, Tischer C, Elofsson A, von Heijne G, Thiele C, Pepperkok R, Wieland F, Brügger B (2012) Molecular recognition of a single sphingolipid species by a protein’s transmembrane domain. Nature 481:525–529CrossRefGoogle Scholar
  18. Das N, Dai J, Hung I, Rajagopalan MR, Zhou HX, Cross TA (2015) Structure of CrgA, a cell division structural and regulatory protein from Mycobacterium tuberculosis, in lipid bilayers. Proc Natl Acad Sci USA 112:E119–E126CrossRefGoogle Scholar
  19. Davis JH, Jeffrey KR, Bloom M, Valic MI, Higgs TP (1976) Quadrupolar echo deuteron magnetic resonance spectroscopy in ordered hydrocarbon chains. Chem Phys Lett 42:390–394CrossRefGoogle Scholar
  20. Derganc J, Antonny B, Copic A (2013) Membrane bending: the power of protein imbalance. Trends Biochem Sci 38:576–584CrossRefGoogle Scholar
  21. Diaz-Horta O, Cintado A, Fernandez-De-Cossio ME, Nazabal M, Ferrer A, Roca J, Camacho H, Benitez J, Ale M, Villarreal A, Molina G, Vera M, Cabrera-Rode E, Novoa L (2010) Relationship of type 1 diabetes to ancestral proportions and HLA DR/DQ alleles in a sample of the admixed Cuban population. Ann Hum Biol 37:778–788CrossRefGoogle Scholar
  22. Dixon AM, Roy S (2019) Role of membrane environment and membrane-spanning protein regions in assembly and function of the class II major histocompatibility complex. Hum Immunol 80:5–14CrossRefGoogle Scholar
  23. Dixon AM, Drake L, Hughes KT, Sargent E, Hunt D, Harton JA, Drake JR (2014) Differential transmembrane domain GXXXG motif pairing impacts major histocompatibility complex (MHC) class II structure. J Biol Chem 289:11695–11703CrossRefGoogle Scholar
  24. Drake LA, Drake JR (2016) A triad of molecular regions contribute to the formation of two distinct MHC class II conformers. Mol Immunol 74:59–70CrossRefGoogle Scholar
  25. Dufourc EJ (2008) Sterols and membrane dynamics. J Chem Biol 1:63–77CrossRefGoogle Scholar
  26. Fung BM, Khitrin AK, Ermolaev K (2000) An improved broadband decoupling sequence for liquid crystals and solids. J Magn Reson 142:97–101CrossRefGoogle Scholar
  27. Gambelunghe G, Brozzetti A, Ghaderi M, Candeloro P, Tortoioli C, Falorni A (2007) MICA gene polymorphism in the pathogenesis of type 1 diabetes. Ann NY Acad Sci 1110:92–98CrossRefGoogle Scholar
  28. Gopinath T, Mote KR, Veglia G (2015) Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples. J Biomol NMR 62:53–61CrossRefGoogle Scholar
  29. Grage SL, Afonin S, Kara S, Buth G, Ulrich AS (2016) Membrane thinning and thickening induced by membrane-active amphipathic peptides. Front Cell Dev Biol 4:65CrossRefGoogle Scholar
  30. Hallock KJ, Lee DK, Ramamoorthy A (2003) MSI-78, an analogue of the magainin antimicrobial peptides, disrupts lipid bilayer structure via positive curvature strain. Biophys J 84:3052–3060CrossRefGoogle Scholar
  31. Harmouche N, Bechinger B (2018) Lipid-mediated interactions between the amphipathic antimicrobial peptides magainin 2 and PGLa in phospholipid bilayers. Biophys J 115:1033–1044CrossRefGoogle Scholar
  32. Harzer U (2000) Untersuchungen zur topologie und struktur von membranproteinen. PhD, Technical University. MunichGoogle Scholar
  33. Hille B, Dickson EJ, Kruse M, Vivas O, Suh BC (2015) Phosphoinositides regulate ion channels. Biochim Biophys Acta 1851:844–856CrossRefGoogle Scholar
  34. Holt A, Rougier L, Reat V, Jolibois F, Saurel O, Czaplicki J, Killian JA, Milon A (2010) Order parameters of a transmembrane helix in a fluid bilayer: case study of a WALP peptide. Biophys J 98:1864–1872CrossRefGoogle Scholar
  35. Hong M (2006) Oligomeric structure, dynamics, and orientation of membrane proteins from solid-state NMR. Structure 14:1731–1740CrossRefGoogle Scholar
  36. Huang HW (2000) Action of antimicrobial peptides: two-state model. Biochemistry 39:8347–8352CrossRefGoogle Scholar
  37. Itkin A, Salnikov ES, Aisenbrey C, Raya J, Raussens V, Ruysschaert JM, Bechinger B (2017) Evidence for heterogeneous conformations of the gamma cleavage site within the amyloid precursor proteins transmembrane domain ACS. Omega 2:6525–6534CrossRefGoogle Scholar
  38. Jenne N, Frey K, Brugger B, Wieland FT (2002) Oligomeric state and stoichiometry of p24 proteins in the early secretory pathway. J Biol Chem 277:46504–46511CrossRefGoogle Scholar
  39. Kemayo Koumkoua P, Aisenbrey C, Salnikov ES, Rifi O, Bechinger B (2014) On the design of supramolecular assemblies made of peptides and lipid bilayers. J. Peptide Sci. 20:526–536CrossRefGoogle Scholar
  40. Kim C, Spano J, Park EK, Wi S (2009) Evidence of pores and thinned lipid bilayers induced in oriented lipid membranes interacting with the antimicrobial peptides, magainin-2 and aurein-3.3. Biochim Biophys Acta 1788:1482–1496CrossRefGoogle Scholar
  41. King G, Dixon AM (2010) Evidence for role of transmembrane helix–helix interactions in the assembly of the class II major histocompatibility complex. Mol BioSyst 6:1650–1661CrossRefGoogle Scholar
  42. Langer JD, Roth CM, Bethune J, Stoops EH, Brugger B, Herten DP, Wieland FT (2008) A conformational change in the alpha-subunit of coatomer induced by ligand binding to gamma-COP revealed by single-pair FRET. Traffic 9:597–607CrossRefGoogle Scholar
  43. Loudet C, Khemtemourian L, Aussenac F, Gineste S, Achard MF, Dufourc EJ (2005) Bicelle membranes and their use for hydrophobic peptide studies by circular dichroism and solid state NMR. Biochem Biophys Acta 1724:315–323CrossRefGoogle Scholar
  44. Marquette A, Bechinger B (2018) Biophysical investigations elucidating the mechanisms of action of antimicrobial peptides and their synergism. Biomolecules 8:E18CrossRefGoogle Scholar
  45. Michalek M, Salnikov E, Werten S, Bechinger B (2013) Structure and topology of the huntingtin 1-17 membrane anchor by a combined solution and solid-state NMR approach. Biophys J 105:699–710CrossRefGoogle Scholar
  46. Nagle JF, Tristram-Nagle S (2000) Structure of lipid bilayers. Biochim Biophys Acta 1469:159–195CrossRefGoogle Scholar
  47. Painter CA, Stern LJ (2012) Conformational variation in structures of classical and non-classical MHCII proteins and functional implications. Immunol Rev 250:144–157CrossRefGoogle Scholar
  48. Palsdottir H, Lojero CG, Trumpower BL, Hunte C (2003) Structure of the yeast cytochrome bc1 complex with a hydroxyquinone anion Qo site inhibitor bound. J Biol Chem 278:31303–31311CrossRefGoogle Scholar
  49. Perrone B, Miles AJ, Salnikov ES, Wallace B, Bechinger B (2014) Lipid-interactions of the LAH4, a peptide with antimicrobial and nucleic transfection activities Eur. Biophys J 43:499–507Google Scholar
  50. Ramamoorthy A, Lee DK, Narasimhaswamy T, Nanga RPR (2010) Cholesterol reduces pardaxin’s dynamics-a barrel-stave mechanism of membrane disruption investigated by solid-state NMR. Biochim Biophys Acta 1798:223–227CrossRefGoogle Scholar
  51. Rance M, Byrd RA (1983) Obtaining high-fidelity spin-1/2 powder spectra in anisotropic media: phase-cycled Hahn echo spectroscopy. J Magn Reson 52:221–240Google Scholar
  52. Raya J, Perrone B, Bechinger B, Hirschinger J (2011) Chemical shift powder spectra obtained by using rotor-directed exchange of orientations cross-polarization (RODEO-CP). Chem Phys Lett 508:155–164CrossRefGoogle Scholar
  53. Reinhard C, Harter C, Bremser M, Brugger B, Sohn K, Helms JB, Wieland F (1999) Receptor-induced polymerization of coatomer. Proc Natl Acad Sci USA 96:1224–1228CrossRefGoogle Scholar
  54. Resende JM, Verly RM, Aisenbrey C, Amary C, Bertani P, Pilo-Veloso D, Bechinger B (2014) Membrane interactions of phylloseptin-1, -2, and -3 peptides by oriented solid-state NMR spectroscopy. Biophys J 107:901–911CrossRefGoogle Scholar
  55. Russ WP, Engelman DM (2000) The GxxxG motif: a framework for transmembrane helix-helix association. J Mol Biol 296:911–919CrossRefGoogle Scholar
  56. Salnikov E, Bertani P, Raap J, Bechinger B (2009a) Analysis of the amide (15)N chemical shift tensor of the C(alpha) tetrasubstituted constituent of membrane-active peptaibols, the alpha-aminoisobutyric acid residue, compared to those of di- and tri-substituted proteinogenic amino acid residues. J Biomol NMR 45:373–387CrossRefGoogle Scholar
  57. Salnikov ES, Mason AJ, Bechinger B (2009b) Membrane order perturbation in the presence of antimicrobial peptides by 2H solid-state NMR spectroscopy. Biochimie 91:734–743CrossRefGoogle Scholar
  58. Salnikov E, Aisenbrey C, Vidovic V, Bechinger B (2010) Solid-state NMR approaches to measure topological equilibria and dynamics of membrane polypeptides. Biochim Biophys Acta 1798:258–265CrossRefGoogle Scholar
  59. Salnikov E, Aisenbrey C, Balandin SV, Zhmak MN, Ovchinnikova AY, Bechinger B (2011) Structure and alignment of the membrane-associated antimicrobial peptide arenicin by oriented solid-state NMR spectroscopy. Biochemistry 50:3784–3795CrossRefGoogle Scholar
  60. Salnikov ES, Aisenbrey C, Anantharamaiah GM, Bechinger B (2019) Solid-state NMR structural investigations of peptide-based nanodiscs and of transmembrane helices in bicellar disc arrangements. Chem Phys Lipid 219:58–71CrossRefGoogle Scholar
  61. Sato T, Tang TC, Reubins G, Fei JZ, Fujimoto T, Kienlen-Campard P, Constantinescu SN, Octave JN, Aimoto S, Smith SO (2009) A helix-to-coil transition at the epsilon-cut site in the transmembrane dimer of the amyloid precursor protein is required for proteolysis. Proc Natl Acad Sci USA 106:1421–1426CrossRefGoogle Scholar
  62. Smith SO, Eilers M, Song D, Crocker E, Ying W, Groesbeek M, Metz G, Ziliox M, Aimoto S (2002) Implications of threonine hydrogen bonding in the glycophorin A transmembrane helix dimer. Biophys J 82:2476–2486CrossRefGoogle Scholar
  63. Stangl M, Schneider D (2015) Functional competition within a membrane: lipid recognition vs. transmembrane helix oligomerization. Biochim Biophys Acta 1848:1886–1896CrossRefGoogle Scholar
  64. Strating JR, Martens GJ (2009) The p24 family and selective transport processes at the ER-Golgi interface. Biol Cell 101:495–509CrossRefGoogle Scholar
  65. Travers P, Blundell TL, Sternberg MJE, Bodmer WF (1984) Structural and evolutionary analysis of HLA-D-region products. Nature 310:235–238CrossRefGoogle Scholar
  66. Tsai S, Santamaria P (2013) MHC class II polymorphisms, autoreactive T-cells, and autoimmunity. Front Immunol 4:321CrossRefGoogle Scholar
  67. Vogt TCB, Ducarme P, Schinzel S, Brasseur R, Bechinger B (2000) The topology of lysine-containing amphipathic peptides in bilayers by CD, solid-state NMR and molecular modelling. Biophys J 79:2644–2656CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institut de Chimie, Université de Strasbourg/CNRS, UMR7177StrasbourgFrance

Personalised recommendations