Skip to main content
SpringerLink
Log in

Structural Investigations of Protein–Lipid Complexes Using Neutron Scattering

  • Protocol
  • First Online:
Lipid-Protein Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2003))

Abstract

Neutron scattering has significant benefits for examining the structure of protein–lipid complexes. Cold (slow) neutrons are nondamaging and predominantly interact with the atomic nucleus, meaning that neutron beams can penetrate deeply into samples, which allows for flexibility in the design of samples studied. Most importantly, there is a strong difference in neutron scattering length (i.e., scattering power) between protium (\( {}_1{}^1H \), 99.98% natural abundance) and deuterium (\( {}_1{}^2H \) or D, 0.015%). Through the mixing of H2O and D2O in the samples and in some cases the deuterium labeling of the biomolecules, components within a complex can be hidden or enhanced in the scattering signal. This enables both the overall structure and the relative distribution of components within a complex to be resolved. Lipid–protein complexes are most commonly studied using neutron reflectometry (NR) and small angle neutron scattering (SANS). In this review the methodologies to produce and examine a variety of model biological membrane systems using SANS and NR are detailed. These systems include supported lipid bilayers derived from vesicle dispersions or Langmuir–Blodgett deposition, tethered bilayer systems, membrane protein–lipid complexes and polymer wrapped lipid nanodiscs. The three key stages of any SANS/NR study on model membrane systems—sample preparation, data collection, and analysis—are described together with some background on the techniques themselves.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Change history

  • 21 April 2020

    This chapter was inadvertently published with the expansion of the term “MNB” printed incorrectly as “N-Methyl-N-nitrosobenzamide” under section 2.5. Instead, it should have been “Methyl 4- nitrobenzenesulfonate.” This correction has been updated in the chapter.

References

  1. Foglia F, Hazael R, Simeoni GG, Appavou M-S, Moulin M, Haertlein M, Forsyth VT, Seydel T, Daniel I, Meersman F, McMillan PF (2015) Water dynamics in Shewanella oneidensis at ambient and high pressure using quasi-elastic neutron scattering. Sci Rep 6:18862

    Google Scholar 

  2. Lopez-Rubio A, Gilbert EP (2009) Neutron scattering: a natural tool for food science and technology research. Trends Food Sci Technol 20:576–586

    CAS  Google Scholar 

  3. Heinrich F, Lösche M (2014) Zooming in on disordered systems: neutron reflection studies of proteins associated with fluid membranes. Biochim Biophys Acta 1838:2341–2349

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Neylon C (2008) Small angle neutron and X-ray scattering in structural biology: recent examples from the literature. Eur Biophys J 37:28–30

    Google Scholar 

  5. Lakey JH (2009) Neutrons for biologists: a beginner’s guide, or why you should consider using neutrons. J R Soc Interface 6(Suppl 5):S567–S573

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Le Brun AP, Clifton LA, Holt SA, Holden PJ, Lakey JH (2015) Deuterium labelling strategies for creating contrast in structure-function studies of model bacterial outer membranes using neutron reflectometry. Methods Enzymol 566:231–252

    PubMed  Google Scholar 

  7. Dunne O, Weidenhaupt M, Callow P, Martel A, Moulin M, Perkins SJ, Haertlein M, Forsyth VT (2017) Matchout deuterium labelling of proteins for small-angle neutron scattering studies using prokaryotic and eukaryotic expression systems and high cell-density cultures. Eur Biophys J 46:425–432

    CAS  PubMed  Google Scholar 

  8. Clifton LA, Holt SA, Hughes AV, Daulton EL, Arunmanee W, Heinrich F, Khalid S, Jefferies D, Charlton TR, Webster JRP, Kinane CJ, Lakey JH (2015) An accurate in vitro model of the E. coli envelope. Angew Chem Int Ed 54:11952–11955

    CAS  Google Scholar 

  9. Clifton LA, Skoda MWA, Le Brun AP, Ciesielski F, Kuzmenko I, Holt SA, Lakey JH (2015) Effect of divalent cation removal on the structure of gram-negative bacterial outer membrane models. Langmuir 31:404–412

    CAS  PubMed  Google Scholar 

  10. Fragneto G, Graner F, Charitat T, Dubos P, Magiste M (2000) Interaction of the third helix of Antennapedia homeodomain with a deposited phospholipid bilayer: a neutron reflectivity structural study. Langmuir 1:4581–4588

    Google Scholar 

  11. Fragneto G, Charitat T, Daillant J (2012) Floating lipid bilayers: models for physics and biology. Eur Biophys J Biophys Lett 41:863–874

    CAS  Google Scholar 

  12. Gerelli Y, Porcar L, Fragneto G (2012) Lipid rearrangement in DSPC/DMPC bilayers: a neutron reflectometry study. Langmuir 28:15922–15928

    CAS  PubMed  Google Scholar 

  13. Wacklin HP (2011) Composition and asymmetry in supported membranes formed by vesicle fusion. Langmuir 27:7698–7707

    CAS  PubMed  Google Scholar 

  14. Clifton LA, Skoda MW, Daulton EL, Hughes AV, Le Brun AP, Lakey JH, Holt SA (2013) Asymmetric phospholipid: lipopolysaccharide bilayers; a Gram-negative bacterial outer membrane mimic. J R Soc Interface 10:20130810

    PubMed  PubMed Central  Google Scholar 

  15. Clifton LA, Ciesielski F, Skoda MWA, Paracini N, Holt SA, Lakey JH (2016) The effect of lipopolysaccharide core oligosaccharide size on the electrostatic binding of antimicrobial proteins to models of the gram negative bacterial outer membrane. Langmuir 32:3485–3494

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Vacklin HP, Tiberg F, Fragneto G, Thomas RK (2005) Phospholipase A2 hydrolysis of supported phospholipid bilayers: a neutron reflectivity and ellipsometry study. Biochemistry 44:2811–2821

    CAS  PubMed  Google Scholar 

  17. Hoogerheide DP, Noskov SY, Jacobs D, Bergdoll L, Silin V, Worcester DL, Abramson J, Nanda H, Rostovtseva TK, Bezrukov SM (2017) Structural features and lipid binding domain of tubulin on biomimetic mitochondrial membranes. Proc Natl Acad Sci 114:E3622–E3631

    CAS  PubMed  Google Scholar 

  18. Foglia F, Lawrence MJ, Barlow DJ (2015) Studies of model biological and bio-mimetic membrane structure: reflectivity vs diffraction, a critical comparison. Curr Opin Colloid Interface Sci 20:235–243

    CAS  Google Scholar 

  19. Wacklin HP (2010) Neutron reflection from supported lipid membranes. Curr Opin Colloid Interface Sci 15:445–454

    CAS  Google Scholar 

  20. Sivia DS (2011) Elementary scattering theory, 1st edn. Oxford University Press, Oxford

    Google Scholar 

  21. Kern W, Soc JE (1990) The evolution of silicon wafer cleaning technology. J Electrochem Soc 137:1887–1892

    CAS  Google Scholar 

  22. Keller CA, Glasmästar K, Zhdanov VP, Kasemo B (2000) Formation of supported membranes from vesicles. Phys Rev Lett 84:5443–5446

    CAS  PubMed  Google Scholar 

  23. Richter R, Mukhopadhyay A, Brisson A (2003) Pathways of lipid vesicle deposition on solid surfaces: a combined QCM-D and AFM study. Biophys J 85:3035–3047

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Lind TK, Cárdenas M, Wacklin HP (2014) Formation of supported lipid bilayers by vesicle fusion: effect of deposition temperature. Langmuir 30:7259–7263

    CAS  PubMed  Google Scholar 

  25. Åkesson A, Lind T, Ehrlich N, Stamou D, Wacklin H, Cárdenas M (2012) Composition and structure of mixed phospholipid supported bilayers formed by POPC and DPPC. Soft Matter 8:5658–5665

    Google Scholar 

  26. Budvytyte R, Valincius G, Niaura G, Voiciuk V, Mickevicius M, Chapman H, Goh HZ, Shekhar P, Heinrich F, Shenoy S, Lösche M, Vanderah DJ (2013) Structure and properties of tethered bilayer lipid membranes with unsaturated anchor molecules. Langmuir 29:8645–8656

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Junghans A, Köper I (2010) Structural analysis of tethered bilayer lipid membranes. Langmuir 26:11035–11040

    CAS  PubMed  Google Scholar 

  28. Shenoy S, Moldovan R, Fitzpatrick J, Vanderah DJ, Deserno M, Lösche M (2010) In-plane homogeneity and lipid dynamics in tethered bilayer lipid membranes (tBLMs). Soft Matter 6:1263–1274

    CAS  Google Scholar 

  29. McGillivray DJ, Valincius G, Vanderah DJ, Febo-Ayala W, Woodward JT, Heinrich F, Kasianowicz JJ, Lösche M (2007) Molecular-scale structural and functional characterization of sparsely tethered bilayer lipid membranes. Biointerphases 2:21–33

    CAS  PubMed  Google Scholar 

  30. Rossi C, Chopineau J (2007) Biomimetic tethered lipid membranes designed for membrane-protein interaction studies. Eur Biophys J 36:955–965

    CAS  PubMed  Google Scholar 

  31. Purrucker O, Fortig A, Rainer J, Tanaka M (2004) Supported membranes with well-defined polymer tethers—incorporation of cell receptors. ChemPhysChem 5:327–335

    CAS  PubMed  Google Scholar 

  32. Singh S, Junghans A, Tian J, Dubey M, Gnanakaran S, Chlistunoff J, Majewski J (2013) Polyelectrolyte multilayers as a platform for pH-responsive lipid bilayers. Soft Matter 9:8938–8948

    CAS  Google Scholar 

  33. Smith HL, Jablin MS, Vidyasagar A, Saiz J, Watkins E, Toomey R, Hurd AJ, Majewski J (2009) Model lipid membranes on a tunable polymer cushion. Phys Rev Lett 102:1–4

    Google Scholar 

  34. Tanaka M, Sackmann E (2005) Polymer-supported membranes as models of the cell surface. Nature 437:656–663

    CAS  PubMed  Google Scholar 

  35. Junghans A, Watkins EB, Barker RD, Singh S, Waltman MJ, Smith HL, Pocivavsek L, Majewski J (2015) Analysis of biosurfaces by neutron reflectometry: from simple to complex interfaces. Biointerphases 10:19014

    Google Scholar 

  36. Jablin MS, Zhernenkov M, Toperverg BP, Dubey M, Smith HL, Vidyasagar A, Toomey R, Hurd AJ, Majewski J (2011) In-plane correlations in a polymer-supported lipid membrane measured by off-specular neutron scattering. Phys Rev Lett 106:1–4

    Google Scholar 

  37. Tabaei SR, Vafaei S, Cho N-J (2015) Fabrication of charged membranes by the solvent-assisted lipid bilayer (SALB) formation method on SiO2 and Al2O3. Phys Chem Chem Phys 17:11546–11552

    CAS  PubMed  Google Scholar 

  38. Heinrich F, Ng T, Vanderah DJ, Shekhar P, Mihailescu M, Nanda H, Losche M (2009) A new lipid anchor for sparsely tethered bilayer lipid membranes. Langmuir 25:4219–4229

    CAS  PubMed  Google Scholar 

  39. Barros M, Heinrich F, Datta SAK, Rein A, Karageorgos I, Nanda H, Lösche M (2016) Membrane binding of HIV-1 matrix protein: dependence on bilayer composition and protein lipidation. J Virol 90:4544–4555. https://doi.org/10.1128/JVI.02820-15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Hughes AV, Howse JR, Dabkowska A, Jones RAL, Lawrence MJ, Roser SJ (2008) Floating lipid bilayers deposited on chemically grafted phosphatidylcholine surfaces. Langmuir 24:1989–1999

    CAS  PubMed  Google Scholar 

  41. Giess F, Friedrich MG, Heberle J, Naumann RL, Knoll W (2004) The protein-tethered lipid bilayer: a novel mimic of the biological membrane. Biophys J 87:3213–3220

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Shen HH, Leyton DL, Shiota T, Belousoff MJ, Noinaj N, Lu J, Holt SA, Tan K, Selkrig J, Webb CT, Buchanan SK, Martin LL, Lithgow T (2014) Reconstitution of a nanomachine driving the assembly of proteins into bacterial outer membranes. Nat Commun 5:1–10

    Google Scholar 

  43. Kang E, Park JW, McClellan SJ, Kim JM, Holland DP, Lee GU, Franses EI, Park K, Thompson DH (2007) Specific adsorption of histidine-tagged proteins on silica surfaces modified with Ni2+/NTA-derivatized poly(ethylene glycol). Langmuir 23:6281–6288

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Hatty CR, Le Brun AP, Lake V, Clifton L a, Liu GJ, James M, Banati RB (2014) Investigating the interactions of the 18kDa translocator protein and its ligand PK11195 in planar lipid bilayers. Biochim Biophys Acta 1838:1019–1030

    CAS  PubMed  Google Scholar 

  45. Vacklin HP, Tiberg F, Thomas RK (2005) Formation of supported phospholipid bilayers via co-adsorption with β-D-dodecyl maltoside. Biochim Biophys Acta Biomembr 1668:17–24

    CAS  Google Scholar 

  46. Parratt LG (1954) Surface studies of solids by total reflection of x-rays. Phys Rev 95:359–369

    Google Scholar 

  47. Abel F (1950) La theorie generale des couches minces. J Phys Radium 22:307–309

    Google Scholar 

  48. Born M, Wolf E (1970) Principles of optics. Pergamon Press, Oxford

    Google Scholar 

  49. Als-Nielsen J, McMorrow D (2011) Elements of modern X-ray physics. Wiley Interscience, Hoboken, NJ

    Google Scholar 

  50. Majkrzak CF, Berk NF, Perez-Salas UA (2003) Phase-sensitive neutron reflectometry. Langmuir 19:7796–7810

    CAS  Google Scholar 

  51. Holt SA, Le Brun AP, Majkrzak CF, McGillivray DJ, Heinrich F, Loesche M, Lakey JH (2009) An ion-channel-containing model membrane: structural determination by magnetic contrast neutron reflectometry. Soft Matter 5:2576–2586

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Shekhar P, Nanda H, Lösche M, Heinrich F (2011) Continuous distribution model for the investigation of complex molecular architectures near interfaces with scattering techniques. J Appl Phys 110:1–12

    Google Scholar 

  53. Stidder B, Fragneto G, Roser SJ (2005) Effect of low amounts of cholesterol on the swelling behavior of floating bilayers. Langmuir 21:9187–9193. http://www.ncbi.nlm.nih.gov/pubmed/16171350

    CAS  PubMed  Google Scholar 

  54. Clifton LA, Skoda MWA, Daulton EL, Hughes AV, Le Brun AP, Lakey JH, Holt SA (2013) Gram-negative bacterial outer membrane mimic asymmetric phospholipid: lipopolysaccharide bilayers: a Gram-negative bacterial outer membrane mimic. J R Soc Interface 10:20130810

    PubMed  PubMed Central  Google Scholar 

  55. Clifton LA, Sanders M, Kinane C, Arnold T, Edler KJ, Neylon C, Green RJ, Frazier RA (2012) The role of protein hydrophobicity in thionin-phospholipid interactions: a comparison of α1 and α2-purothionin adsorbed anionic phospholipid monolayers. Phys Chem Chem Phys 14:13569–13597

    CAS  PubMed  Google Scholar 

  56. Fernandez DI, Le Brun AP, Lee T-H, Bansal P, Aguilar M-I, James M, Separovic F (2013) Structural effects of the antimicrobial peptide maculatin 1.1 on supported lipid bilayers. Eur Biophys J 42:47–59

    CAS  PubMed  Google Scholar 

  57. Wang CK, Wacklin HP, Craik DJ (2012) Cyclotides insert into lipid bilayers to form membrane pores and destabilize the membrane through hydrophobic and phosphoethanolamine-specific interactions. J Biol Chem 287:43884–43898

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Chenal A, Prongidi-Fix L, Perier A, Aisenbrey C, Vernier G, Lambotte S, Fragneto G, Bechinger B, Gillet D, Forge V, Ferrand M (2009) Deciphering membrane insertion of the diphtheria toxin T domain by specular neutron reflectometry and solid-state NMR spectroscopy. J Mol Biol 391:872–883

    CAS  PubMed  Google Scholar 

  59. Clifton LA, Sanders MR, Hughes AV, Neylon C, Frazier RA, Green RJ (2011) Lipid binding interactions of antimicrobial plant seed defence proteins: puroindoline-a and β-purothionin. Phys Chem Chem Phys 13:17153–17162

    CAS  PubMed  Google Scholar 

  60. Svergun DI, Koch MHJ, Timmins PA, May RP (2013) Small angle X-ray and neutron scattering from solutions of biological macromolecules. Oxford University Press, Oxford, pp 27–64

    Google Scholar 

  61. Zimmer J, Doyle DA, Grossmann JG (2006) Structural characterization and pH-induced conformational transition of full-length KcsA. Biophys J 90:1752–1766

    CAS  PubMed  Google Scholar 

  62. Clifton LA, Johnson CL, Solovyova AS, Callow P, Weiss KL, Ridley H, Le Brun AP, Kinane CJ, Webster JRP, Holt S a, Lakey JH (2012) Low resolution structure and dynamics of a colicin-receptor complex determined by neutron scattering. J Biol Chem 287:337–346

    CAS  PubMed  Google Scholar 

  63. Koutsioubas A (2017) Low-resolution structure of detergent-solubilized membrane proteins from small-angle scattering data. Biophys J 113:2373–2382

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Denisov IG, Sligar SG (2017) Nanodiscs in membrane biochemistry and biophysics. Chem Rev 117:4669–4713

    CAS  PubMed  PubMed Central  Google Scholar 

  65. Skar-Gislinge N, Arleth L (2011) Small-angle scattering from phospholipid nanodiscs: derivation and refinement of a molecular constrained analytical model form factor. Phys Chem Chem Phys 13:3161–3170

    CAS  PubMed  Google Scholar 

  66. Kynde SAR, Skar-Gislinge N, Pedersen MC, Midtgaard SR, Simonsen JB, Schweins R, Mortensen K, Arleth L (2014) Small-angle scattering gives direct structural information about a membrane protein inside a lipid environment. Acta Crystallogr D Biol Crystallogr 70:371–383

    CAS  PubMed  Google Scholar 

  67. Maric S, Skar-Gislinge N, Midtgaard S, Thygesen MB, Schiller J, Frielinghaus H, Moulin M, Haertlein M, Forsyth VT, Pomorski TG, Arleth L (2014) Stealth carriers for low-resolution structure determination of membrane proteins in solution. Acta Crystallogr D Biol Crystallogr 70:317–328

    CAS  PubMed  Google Scholar 

  68. Knowles TJ, Finka R, Smith C, Lin Y-P, Dafforn T, Overduin M (2009) Membrane proteins solubilized intact in lipid containing nanoparticles bounded by styrene maleic acid copolymer. J Am Chem Soc 131:7484–7485

    CAS  PubMed  Google Scholar 

  69. Jamshad M, Charlton J, Lin Y-P, Routledge SJ, Bawa Z, Knowles TJ, Overduin M, Dekker N, Dafforn TR, Bill RM, Poyner DR, Wheatley M (2015) G-protein coupled receptor solubilization and purification for biophysical analysis and functional studies, in the total absence of detergent. Biosci Rep 35:e00188

    PubMed  PubMed Central  Google Scholar 

  70. Morrison KA, Akram A, Mathews A, Khan ZA, Patel JH, Zhou C, Hardy DJ, Moore-Kelly C, Patel R, Odiba V, Knowles TJ, Javed M -u-H, Chmel NP, Dafforn TR, Rothnie AJ (2016) Membrane protein extraction and purification using styrene-maleic acid (SMA) copolymer: effect of variations in polymer structure. Biochem J 473:4349–4360

    CAS  PubMed  Google Scholar 

  71. Lee SC, Knowles TJ, Postis VLG, Jamshad M, Parslow RA, Lin Y-P, Goldman A, Sridhar P, Overduin M, Muench SP, Dafforn TR (2016) A method for detergent-free isolation of membrane proteins in their local lipid environment. Nat Protoc 11:1149–1162

    CAS  PubMed  Google Scholar 

  72. Jamshad M, Grimard V, Idini I, Knowles TJ, Dowle MR, Schofield N, Sridhar P, Lin Y, Finka R, Wheatley M, Thomas ORT, Palmer RE, Overduin M, Govaerts C, Ruysschaert J-M, Edler KJ, Dafforn TR (2015) Structural analysis of a nanoparticle containing a lipid bilayer used for detergent-free extraction of membrane proteins. Nano Res 8:774–789

    CAS  PubMed  Google Scholar 

  73. Hall SCL, Tognoloni C, Price GJ, Klumperman B, Edler KJ, Dafforn TR, Arnold T (2017) The influence of poly(styrene-co-maleic acid) copolymer structure on the properties and self-assembly of SMALP nanodiscs. Biomacromolecules 19(3):761–772

    Google Scholar 

  74. Glatter O (1977) A new method for the evaluation of small-angle scattering data. J Appl Crystallogr 10:415–421

    Google Scholar 

  75. Guinier A (1939) La diffraction des rayons X aux tres petits angles: applications a l’etude de phenomenes ultramicroscopiques. Ann Phys 11:161–237

    Google Scholar 

  76. Fournet G, Guinier A (1955) Eng.Uc.Edu. Goeppert Mayer M (ed). John Wiley and Sons, New York, NY, pp 7–78

    Google Scholar 

  77. Petoukhov MV, Franke D, Shkumatov AV, Tria G, Kikhney AG, Gajda M, Gorba C, Mertens HDT, Konarev PV, Svergun DI (2012) New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Crystallogr 45:342–350

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Moore PB (1980) Small-angle scattering. Information content and error analysis. J Appl Crystallogr 13:168–175

    CAS  Google Scholar 

  79. Grant TD, Luft JR, Carter LG, Matsui T, Weiss TM, Martel A, Snell EH (2015) The accurate assessment of small-angle X-ray scattering data. Acta Crystallogr D Biol Crystallogr 71:45–56

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Pedersen JS (1997) Analysis of small-angle scattering data from colloids and polymer solutions: modeling and least-squares fitting. Adv Colloid Interf Sci 70:171–210

    CAS  Google Scholar 

  81. Svergun DI (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Crystallogr 25:495–503

    CAS  Google Scholar 

  82. Petoukhov MV, Konarev PV, Kikhney AG, Svergun DI (2007) ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis. J Appl Crystallogr 40:223–228

    Google Scholar 

  83. Rambo RP, Tainer JA (2013) Accurate assessment of mass, models and resolution by small-angle scattering. Nature 496:477–481

    CAS  PubMed  PubMed Central  Google Scholar 

  84. Hansen S (2000) Bayesian estimation of hyperparameters for indirect Fourier transformation in small-angle scattering. J Appl Cryst 33:1415–1421

    CAS  Google Scholar 

  85. Vestergaard B, Hansen S (2006) Application of Bayesian analysis to indirect Fourier transformation in small-angle scattering. J Appl Crystallogr 39:797–804

    CAS  Google Scholar 

  86. Engelman DM, Moore PB (1975) Determination of quaternary structure by small angle neutron scattering. Annu Rev Biophys Bioeng 4:219–241

    CAS  PubMed  Google Scholar 

  87. Whitten AE, Cai S, Trewhella J (2008) MULCh: modules for the analysis of small-angle neutron contrast variation data from biomolecular assemblies. J Appl Crystallogr 41:222–226

    CAS  Google Scholar 

  88. Kline SR (2006) Reduction and analysis of SANS and USANS data using IGOR Pro. J Appl Crystallogr 39:895–900

    CAS  Google Scholar 

  89. Svergun DI (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J 76:2879–2886

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Petoukhov MV, Svergun DI (2005) Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys J 89:1237–1250

    CAS  PubMed  PubMed Central  Google Scholar 

  91. Franke D, Svergun DI (2009) DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J Appl Crystallogr 42:342–346

    CAS  PubMed  PubMed Central  Google Scholar 

  92. Svergun DI, Petoukhov MV, Koch MHJ (2001) Determination of domain structure of proteins from x-ray solution scattering. Biophys J 80:2946–2953

    CAS  PubMed  PubMed Central  Google Scholar 

  93. Svergun DI, Richard S, Koch MH, Sayers Z, Kuprin S, Zaccai G (1998) Protein hydration in solution: experimental observation by x-ray and neutron scattering. Proc Natl Acad Sci U S A 95:2267–2272

    CAS  PubMed  PubMed Central  Google Scholar 

  94. Curtis JE, Raghunandan S, Nanda H, Krueger S (2012) SASSIE: a program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints. Comput Phys Commun 183:382–389

    CAS  Google Scholar 

  95. Tjioe E, Heller WT (2007) ORNL_SAS: software for calculation of small-angle scattering intensities of proteins and protein complexes. J Appl Crystallogr 40:782–785

    CAS  Google Scholar 

  96. Schneidman-Duhovny D, Hammel M, Sali A (2010) FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res 38:540–544

    Google Scholar 

  97. Skar-Gislinge N, Kynde SAR, Denisov IG, Ye X, Lenov I, Sligar SG, Arleth L (2015) Small-angle scattering determination of the shape and localization of human cytochrome P450 embedded in a phospholipid nanodisc environment. Acta Crystallogr D Biol Crystallogr 71:2412–2421

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

L.A.C. would like to thank Max Skoda, Nicolò Paracini, Martynas Gavutis, Robert Dalgliesh, Sophie Ayscough, and John Webster for helpful discussions and advice; Filip Ciesielski for providing membrane structure diagrams; and Arwel Hughes for fitting software and associated error estimation functions.

Certain commercial materials, equipment, and instruments are identified in this work to describe the experimental procedure as completely as possible. In no case does such an identification imply a recommendation or endorsement by NIST, nor does it imply that the materials, equipment, or instrument identified are necessarily the best available for the purpose.

Author information

Authors and Affiliations

  1. Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot, Oxfordshire, UK

    Luke A. Clifton & Najet Mahmoudi

  2. School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK

    Stephen C. L. Hall & Timothy J. Knowles

  3. Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA

    Frank Heinrich

  4. National Institute of Standards and Technology Centre for Neutron Research, Gaithersburg, MD, USA

    Frank Heinrich

  5. Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK

    Jeremy H. Lakey

Authors
  1. Luke A. Clifton
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stephen C. L. Hall
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Najet Mahmoudi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Timothy J. Knowles
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Frank Heinrich
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jeremy H. Lakey
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Luke A. Clifton or Jeremy H. Lakey .

Editor information

Editors and Affiliations

  1. Department of Biophysics, Institute of Biology, FB10 and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany

    Jörg H. Kleinschmidt

Rights and permissions

Reprints and permissions

Copyright information

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

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Clifton, L.A., Hall, S.C.L., Mahmoudi, N., Knowles, T.J., Heinrich, F., Lakey, J.H. (2019). Structural Investigations of Protein–Lipid Complexes Using Neutron Scattering. In: Kleinschmidt, J. (eds) Lipid-Protein Interactions. Methods in Molecular Biology, vol 2003. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9512-7_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9512-7_11

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9511-0

  • Online ISBN: 978-1-4939-9512-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation