Experimental Characterization of Protein Complex Structure, Dynamics, and Assembly

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1764)

Abstract

Experimental methods for the characterization of protein complexes have been instrumental in achieving our current understanding of the protein universe and continue to progress with each year that passes. In this chapter, we review some of the most important tools and techniques in the field, covering the important points in X-ray crystallography, cryo-electron microscopy, NMR spectroscopy, and mass spectrometry. Novel developments are making it possible to study large protein complexes at near-atomic resolutions, and we also now have the ability to study the dynamics and assembly pathways of protein complexes across a range of sizes.

Key words

X-ray crystallography Cryo-electron microscopy NMR Mass spectrometry Super-resolution microscopy Quaternary structure 

Notes

Acknowledgment

J.M. is supported by a Medical Research Council Career Development Award (MR/M02122X/1).

References

  1. 1.
    Stanley WM (1935) Isolation of a crystalline protein possessing the properties of tobacco-mosaic virus. Science 81:644–645PubMedCrossRefGoogle Scholar
  2. 2.
    Schrödinger E (1947) What is life? The physical aspect of the living cell. Cambridge University Press, CambridgeGoogle Scholar
  3. 3.
    Dronamraju KR (1999) Erwin Schrödinger and the origins of molecular biology. Genetics 153:1071–1076PubMedPubMedCentralGoogle Scholar
  4. 4.
    Fraenkel-Conrat H, Williams RC (1955) Reconstitution of active tobacco mosaic virus from its inactive protein and nucleic acid components. Proc Natl Acad Sci U S A 41:690–698. https://doi.org/10.1073/pnas.41.10.690 PubMedPubMedCentralCrossRefGoogle Scholar
  5. 5.
    Perutz MF, Rossmann MG, Cullis AF et al (1960) Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis. Nature 185:416–422PubMedCrossRefGoogle Scholar
  6. 6.
    Schluenzen F, Tocilj A, Zarivach R et al (2000) Structure of functionally activated small ribosomal subunit at 3.3Å resolution. Cell 102:615–623. https://doi.org/10.1016/S0092-8674(00)00084-2 PubMedCrossRefGoogle Scholar
  7. 7.
    Ramakrishnan V, Wimberly BT, Brodersen DE et al (2000) Structure of the 30S ribosomal subunit. Nature 407:327–339. https://doi.org/10.1038/35030006 PubMedCrossRefGoogle Scholar
  8. 8.
    Ban N, Nissen P, Hansen J et al (2000) The complete atomic structure of the large ribosomal subunit at 2.4Å resolution. Science 289:905–920. https://doi.org/10.1126/science.289.5481.905 PubMedCrossRefGoogle Scholar
  9. 9.
    Fields S, Song O (1989) A novel genetic system to detect protein-protein interactions. Nature 340:245–246. https://doi.org/10.1038/340245a0 PubMedCrossRefGoogle Scholar
  10. 10.
    Rajagopala SV, Sikorski P, Kumar A et al (2014) The binary protein-protein interaction landscape of Escherichia coli. Nat Biotechnol 32:285–290PubMedPubMedCentralCrossRefGoogle Scholar
  11. 11.
    Karas M, Bachmann D, Hillenkamp F (1985) Influence of the wavelength in high-irradiance ultraviolet laser desorption mass spectrometry of organic molecules. Anal Chem 57:2935–2939. https://doi.org/10.1021/ac00291a042 CrossRefGoogle Scholar
  12. 12.
    Fenn JB, Mann M, Meng CK et al (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64–71. https://doi.org/10.1126/science.2675315 PubMedCrossRefGoogle Scholar
  13. 13.
    Rosano GL, Ceccarelli EA (2014) Recombinant protein expression in Escherichia coli: advances and challenges. Front Microbiol. https://doi.org/10.3389/fmicb.2014.00172
  14. 14.
    Wells JN, Bergendahl LT, Marsh JA (2016) Operon gene order is optimized for ordered protein complex assembly. Cell Rep 14:679–685. https://doi.org/10.1016/j.celrep.2015.12.085 PubMedPubMedCentralCrossRefGoogle Scholar
  15. 15.
    Shieh Y-W, Minguez P, Bork P et al (2015) Operon structure and cotranslational subunit association direct protein assembly in bacteria. Science 350:678–680. https://doi.org/10.1126/science.aac8171 PubMedCrossRefGoogle Scholar
  16. 16.
    Poulsen C, Holton S, Geerlof A et al (2010) Stoichiometric protein complex formation and over-expression using the prokaryotic native operon structure. FEBS Lett 584:669–674. https://doi.org/10.1016/j.febslet.2009.12.057 PubMedCrossRefGoogle Scholar
  17. 17.
    Ni QZ, Daviso E, Can TV et al (2013) High frequency dynamic nuclear polarization. Acc Chem Res 46:1933–1941. https://doi.org/10.1021/ar300348n PubMedPubMedCentralCrossRefGoogle Scholar
  18. 18.
    Jia B, Jeon CO (2016) High-throughput recombinant protein expression in Escherichia coli: current status and future perspectives. Open Biol 6:160196. https://doi.org/10.1098/rsob.160196 PubMedPubMedCentralCrossRefGoogle Scholar
  19. 19.
    Norimatsu Y, Hasegawa K, Shimizu N, Toyoshima C (2017) Protein–phospholipid interplay revealed with crystals of a calcium pump. Nature 545:193–198. https://doi.org/10.1038/nature22357 PubMedCrossRefGoogle Scholar
  20. 20.
    Bragg WH, Bragg WL (1913) The reflection of X-rays by crystals. Proc R Soc Math Phys Eng Sci 88:428–438. https://doi.org/10.1098/rspa.1913.0040 CrossRefGoogle Scholar
  21. 21.
    Shi Y (2014) A glimpse of structural biology through X-ray crystallography. Cell 159:995–1014. https://doi.org/10.1016/j.cell.2014.10.051 PubMedCrossRefGoogle Scholar
  22. 22.
    Neutze R, Wouts R, van der Spoel D et al (2000) Potential for biomolecular imaging with femtosecond X-ray pulses. Nature 406:752–757. https://doi.org/10.1038/35021099 PubMedCrossRefGoogle Scholar
  23. 23.
    Taylor G (2003) The phase problem. Acta Crystallogr D Biol Crystallogr 59:1881–1890. https://doi.org/10.1107/S0907444903017815 PubMedCrossRefGoogle Scholar
  24. 24.
    Robertson JM (1936) An X-ray study of the phthalocyanines. Part II. Quantitative structure determination of the metal-free compound. J Chem Soc:1195–1209Google Scholar
  25. 25.
    Dauter Z (2005) Use of polynuclear metal clusters in protein crystallography. Comptes Rendus Chim 8:1808–1814. https://doi.org/10.1016/j.crci.2005.02.032 CrossRefGoogle Scholar
  26. 26.
    Nozawa K, Schneider TR, Cramer P (2017) Core Mediator structure at 3.4 Å extends model of transcription initiation complex. Nature 545:248–251. https://doi.org/10.1038/nature22328 PubMedCrossRefGoogle Scholar
  27. 27.
    Hendrickson W (1991) Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 254:51–58. https://doi.org/10.1126/science.1925561 PubMedCrossRefGoogle Scholar
  28. 28.
    Berman HM, Westbrook J, Feng Z et al (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242PubMedPubMedCentralCrossRefGoogle Scholar
  29. 29.
    McCoy AJ, Grosse-Kunstleve RW, Adams PD et al (2007) Phaser crystallographic software. J Appl Crystallogr 40:658–674. https://doi.org/10.1107/S0021889807021206 PubMedPubMedCentralCrossRefGoogle Scholar
  30. 30.
    Winn MD, Ballard CC, Cowtan KD et al (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67:235–242. https://doi.org/10.1107/S0907444910045749 PubMedPubMedCentralCrossRefGoogle Scholar
  31. 31.
    Merk A, Bartesaghi A, Banerjee S et al (2016) Breaking cryo-EM resolution barriers to facilitate drug discovery. Cell 165:1698–1707. https://doi.org/10.1016/j.cell.2016.05.040 PubMedPubMedCentralCrossRefGoogle Scholar
  32. 32.
    Bai X, McMullan G, Scheres SH (2015) How cryo-EM is revolutionizing structural biology. Trends Biochem Sci 40:49–57. https://doi.org/10.1016/j.tibs.2014.10.005 PubMedCrossRefGoogle Scholar
  33. 33.
    McMullan G, Chen S, Henderson R, Faruqi AR (2009) Detective quantum efficiency of electron area detectors in electron microscopy. Ultramicroscopy 109:1126–1143. https://doi.org/10.1016/j.ultramic.2009.04.002 PubMedPubMedCentralCrossRefGoogle Scholar
  34. 34.
    Dainty JC, Shaw R (1975) Image science, principles, analysis and evaluation of photographic type imaging processes. Academic, LondonGoogle Scholar
  35. 35.
    McMullan G, Clark AT, Turchetta R, Faruqi AR (2009) Enhanced imaging in low dose electron microscopy using electron counting. Ultramicroscopy 109:1411–1416. https://doi.org/10.1016/j.ultramic.2009.07.004 PubMedPubMedCentralCrossRefGoogle Scholar
  36. 36.
    Danev R, Buijsse B, Khoshouei M et al (2014) Volta potential phase plate for in-focus phase contrast transmission electron microscopy. Proc Natl Acad Sci U S A 111:15635–15640. https://doi.org/10.1073/pnas.1418377111 PubMedPubMedCentralCrossRefGoogle Scholar
  37. 37.
    Danev R, Baumeister W (2016) Cryo-EM single particle analysis with the Volta phase plate. elife 5:1–14. https://doi.org/10.7554/eLife.13046 CrossRefGoogle Scholar
  38. 38.
    Khoshouei M, Radjainia M, Baumeister W, Danev R (2017) Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate. Nat Commun 8:16099. https://doi.org/10.1038/ncomms16099 PubMedPubMedCentralCrossRefGoogle Scholar
  39. 39.
    Bai X, Fernandez IS, McMullan G, Scheres SH (2013) Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. elife. https://doi.org/10.7554/eLife.00461
  40. 40.
    Li X, Mooney P, Zheng S et al (2013) Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods 10:584–590PubMedPubMedCentralCrossRefGoogle Scholar
  41. 41.
    Henderson R, Glaeser RM (1985) Quantitative analysis of image contrast in electron micrographs of beam-sensitive crystals. Ultramicroscopy 16:139–150. https://doi.org/10.1016/0304-3991(85)90069-5 CrossRefGoogle Scholar
  42. 42.
    Scheres SHW (2012) RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 180:519–530. https://doi.org/10.1016/j.jsb.2012.09.006 PubMedPubMedCentralCrossRefGoogle Scholar
  43. 43.
    Scheres SHW (2014) Beam-induced motion correction for sub-megadalton cryo-EM particles. elife 3:e03665PubMedPubMedCentralCrossRefGoogle Scholar
  44. 44.
    Sigworth FJ (1998) A maximum-likelihood approach to single-particle image refinement. J Struct Biol 122:328–339. https://doi.org/10.1006/jsbi.1998.4014 PubMedCrossRefGoogle Scholar
  45. 45.
    Scheres SHW, Gao H, Valle M et al (2007) Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nat Methods 4:27–29. https://doi.org/10.1038/nmeth992 PubMedCrossRefGoogle Scholar
  46. 46.
    Lyumkis D, Brilot AF, Theobald DL, Grigorieff N (2013) Likelihood-based classification of cryo-EM images using FREALIGN. J Struct Biol 183:377–388. https://doi.org/10.1016/j.jsb.2013.07.005 PubMedCrossRefGoogle Scholar
  47. 47.
    Punjani A, Rubinstein JL, Fleet DJ, Brubaker MA (2017) cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods 14:290–296. https://doi.org/10.1038/nmeth.4169 PubMedCrossRefGoogle Scholar
  48. 48.
    Wisedchaisri G, Reichow SL, Gonen T (2011) Advances in structural and functional analysis of membrane proteins by electron crystallography. Structure 19:1381–1393. https://doi.org/10.1016/j.str.2011.09.001 PubMedPubMedCentralCrossRefGoogle Scholar
  49. 49.
    Galaz-Montoya JG, Ludtke SJ (2017) The advent of structural biology in situ by single particle cryo-electron tomography. Biophys Rep 3:17–35. https://doi.org/10.1007/s41048-017-0040-0 PubMedPubMedCentralCrossRefGoogle Scholar
  50. 50.
    Bharat TAM, Scheres SHW (2016) Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION. Nat Protoc 11:2054–2065. https://doi.org/10.1038/nprot.2016.124 PubMedPubMedCentralCrossRefGoogle Scholar
  51. 51.
    Leschziner AE, Nogales E (2006) The orthogonal tilt reconstruction method: an approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles. J Struct Biol 153:284–299. https://doi.org/10.1016/j.jsb.2005.10.012 PubMedCrossRefGoogle Scholar
  52. 52.
    Schur FKM, Obr M, Hagen WJH et al (2016) An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. Science 353:506–508. https://doi.org/10.1126/science.aaf9620 PubMedCrossRefGoogle Scholar
  53. 53.
    Pervushin K, Riek R, Wider G, Wüthrich K (1997) Attenuated T2 relaxation by mutual cancellation of dipole–dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc Natl Acad Sci U S A 94:12366–12371. https://doi.org/10.1073/pnas.94.23.12366 PubMedPubMedCentralCrossRefGoogle Scholar
  54. 54.
    Sattler M, Fesik SW (1996) Use of deuterium labeling in NMR: overcoming a sizeable problem. Structure 4:1245–1249. https://doi.org/10.1016/S0969-2126(96)00133-5 PubMedCrossRefGoogle Scholar
  55. 55.
    Ollerenshaw JE, Tugarinov V, Kay LE (2003) Methyl TROSY: explanation and experimental verification. Magn Reson Chem 41:843–852. https://doi.org/10.1002/mrc.1256 CrossRefGoogle Scholar
  56. 56.
    Zhang H, van Ingen H (2016) Isotope-labeling strategies for solution NMR studies of macromolecular assemblies. Curr Opin Struct Biol 38:75–82. https://doi.org/10.1016/j.sbi.2016.05.008 PubMedCrossRefGoogle Scholar
  57. 57.
    Liu D, Xu R, Cowburn D (2009) Segmental isotopic labeling of proteins for nuclear magnetic resonance. Methods Enzymol 462:151–175PubMedCrossRefGoogle Scholar
  58. 58.
    Rosenzweig R, Farber P, Velyvis A et al (2015) ClpB N-terminal domain plays a regulatory role in protein disaggregation. Proc Natl Acad Sci U S A 112:e6872. https://doi.org/10.1073/pnas.1512783112 PubMedPubMedCentralCrossRefGoogle Scholar
  59. 59.
    Frederick KK, Michaelis VK, Caporini MA et al (2017) Combining DNP NMR with segmental and specific labeling to study a yeast prion protein strain that is not parallel in-register. Proc Natl Acad Sci U S A 114:3642–3647. https://doi.org/10.1073/pnas.1619051114 PubMedPubMedCentralCrossRefGoogle Scholar
  60. 60.
    Wells M, Tidow H, Rutherford TJ et al (2008) Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain. Proc Natl Acad Sci U S A 105:5762–5767. https://doi.org/10.1073/pnas.0801353105 PubMedPubMedCentralCrossRefGoogle Scholar
  61. 61.
    Marsh JA, Dancheck B, Ragusa MJ et al (2010) Structural diversity in free and bound states of intrinsically disordered protein phosphatase 1 regulators. Structure 18:1094–1103. https://doi.org/10.1016/j.str.2010.05.015 PubMedPubMedCentralCrossRefGoogle Scholar
  62. 62.
    Mittag T, Marsh J, Grishaev A et al (2010) Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. Structure 18:494–506. https://doi.org/10.1016/j.str.2010.01.020 PubMedPubMedCentralCrossRefGoogle Scholar
  63. 63.
    Marsh JA, Teichmann SA, Forman-Kay JD (2012) Probing the diverse landscape of protein flexibility and binding. Curr Opin Struct Biol 22:643–650. https://doi.org/10.1016/j.sbi.2012.08.008 PubMedCrossRefGoogle Scholar
  64. 64.
    Bozoky Z, Krzeminski M, Muhandiram R et al (2013) Regulatory R region of the CFTR chloride channel is a dynamic integrator of phospho-dependent intra- and intermolecular interactions. Proc Natl Acad Sci U S A 110:E4427–E4436. https://doi.org/10.1073/pnas.1315104110 PubMedPubMedCentralCrossRefGoogle Scholar
  65. 65.
    Andrew ER, Bradbury A, Eades RG (1958) Nuclear magnetic resonance spectra from a crystal rotated at high speed. Nature 182:1659–1659. https://doi.org/10.1038/1821659a0 CrossRefGoogle Scholar
  66. 66.
    Hansen SK, Bertelsen K, Paaske B et al (2015) Solid-state NMR methods for oriented membrane proteins. Prog Nucl Magn Reson Spectrosc 88–89:48–85. https://doi.org/10.1016/j.pnmrs.2015.05.001 PubMedCrossRefGoogle Scholar
  67. 67.
    Loquet A, Sgourakis NG, Gupta R et al (2012) Atomic model of the type III secretion system needle. Nature 486:276–279. https://doi.org/10.1038/nature11079 PubMedPubMedCentralGoogle Scholar
  68. 68.
    Kaplan M, Cukkemane A, van Zundert GCP et al (2015) Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR. Nat Methods 12:5–9. https://doi.org/10.1038/nmeth.3406 CrossRefGoogle Scholar
  69. 69.
    Huang C, Kalodimos CG (2017) Structures of large protein complexes determined by nuclear magnetic resonance spectroscopy. Annu Rev Biophys 46:317–336. https://doi.org/10.1146/annurev-biophys-070816-033701 PubMedCrossRefGoogle Scholar
  70. 70.
    Song H, Hanlon N, Brown NR et al (2001) Phosphoprotein-protein interactions revealed by the crystal structure of kinase-associated phosphatase in complex with phosphoCDK2. Mol Cell 7:615–626PubMedCrossRefGoogle Scholar
  71. 71.
    Krusemark CJ, Frey BL, Belshaw PJ, Smith LM (2009) Modifying the charge state distribution of proteins in electrospray ionization mass spectrometry by chemical derivatization. J Am Soc Mass Spectrom 20:1617–1625. https://doi.org/10.1016/j.jasms.2009.04.017 PubMedPubMedCentralCrossRefGoogle Scholar
  72. 72.
    Radionova A, Filippov I, Derrick PJ (2016) In pursuit of resolution in time-of-flight mass spectrometry: a historical perspective. Mass Spectrom Rev 35:738–757. https://doi.org/10.1002/mas.21470 PubMedCrossRefGoogle Scholar
  73. 73.
    Hu Q, Noll RJ, Li H et al (2005) The Orbitrap: a new mass spectrometer. J Mass Spectrom 40:430–443. https://doi.org/10.1002/jms.856 PubMedCrossRefGoogle Scholar
  74. 74.
    Wilm MS, Mann M (1994) Electrospray and Taylor-Cone theory, Dole’s beam of macromolecules at last? Int J Mass Spectrom Ion Process 136:167–180. https://doi.org/10.1016/0168-1176(94)04024-9 CrossRefGoogle Scholar
  75. 75.
    El-Faramawy A, Siu KWM, Thomson BA (2005) Efficiency of nano-electrospray ionization. J Am Soc Mass Spectrom 16:1702–1707. https://doi.org/10.1016/j.jasms.2005.06.011 PubMedCrossRefGoogle Scholar
  76. 76.
    Sobott F, Hernández H, McCammon MG et al (2002) A tandem mass spectrometer for improved transmission and analysis of large macromolecular assemblies. Anal Chem 74:1402–1407. https://doi.org/10.1021/ac0110552 PubMedCrossRefGoogle Scholar
  77. 77.
    Hernandez H, Robinson CV (2007) Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry. Nat Protoc 2:715–726. https://doi.org/10.1038/nprot.2007.73 PubMedCrossRefGoogle Scholar
  78. 78.
    Sobott F, Benesch JLP, Vierling E, Robinson CV (2002) Subunit exchange of multimeric protein complexes. J Biol Chem 277:38921–38929. https://doi.org/10.1074/jbc.M206060200 PubMedCrossRefGoogle Scholar
  79. 79.
    Laganowsky A, Reading E, Allison TM et al (2014) Membrane proteins bind lipids selectively to modulate their structure and function. Nature 510:172–175. https://doi.org/10.1038/nature13419 PubMedPubMedCentralCrossRefGoogle Scholar
  80. 80.
    Levy ED, Boeri Erba E, Robinson CV, Teichmann SA (2008) Assembly reflects evolution of protein complexes. Nature 453:1262–1265. https://doi.org/10.1038/nature06942 PubMedPubMedCentralCrossRefGoogle Scholar
  81. 81.
    Marsh JA, Hernández H, Hall Z et al (2013) Protein complexes are under evolutionary selection to assemble via ordered pathways. Cell 153:461–470PubMedPubMedCentralCrossRefGoogle Scholar
  82. 82.
    Ahnert SE, Marsh JA, Hernández H et al (2015) Principles of assembly reveal a periodic table of protein complexes. Science 350:aaa2245. https://doi.org/10.1126/science.aaa2245 PubMedCrossRefGoogle Scholar
  83. 83.
    Stengel F, Aebersold R, Robinson CV (2012) Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Mol Cell Proteomics 11:R111.014027–R111.014027. https://doi.org/10.1074/mcp.R111.014027 PubMedCrossRefGoogle Scholar
  84. 84.
    Ward AB, Sali A, Wilson IA (2013) Integrative structural biology. Science 339:913–915. https://doi.org/10.1126/science.1228565 PubMedPubMedCentralCrossRefGoogle Scholar
  85. 85.
    van den Bedem H, Fraser JS (2015) Integrative, dynamic structural biology at atomic resolution - it’s about time. Nat Methods 12:307–318. https://doi.org/10.1038/nmeth.3324 PubMedPubMedCentralCrossRefGoogle Scholar
  86. 86.
    Leitner A, Faini M, Stengel F, Aebersold R (2016) Crosslinking and mass spectrometry: an integrated technology to understand the structure and function of molecular machines. Trends Biochem Sci 41:20–32. https://doi.org/10.1016/j.tibs.2015.10.008 PubMedCrossRefGoogle Scholar
  87. 87.
    Suchanek M, Radzikowska A, Thiele C (2005) Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells. Nat Methods 2:261–268. https://doi.org/10.1038/nmeth752 PubMedCrossRefGoogle Scholar
  88. 88.
    Barysz H, Kim JH, Chen ZA et al (2015) Three-dimensional topology of the SMC2/SMC4 subcomplex from chicken condensin I revealed by cross-linking and molecular modelling. Open Biol 5:150005. https://doi.org/10.1098/rsob.150005 PubMedPubMedCentralCrossRefGoogle Scholar
  89. 89.
    Beck M, Hurt E (2016) The nuclear pore complex: understanding its function through structural insight. Nat Rev Mol Cell Biol. https://doi.org/10.1038/nrm.2016.147
  90. 90.
    Bui KH, von Appen A, DiGuilio AL et al (2013) Integrated structural analysis of the human nuclear pore complex scaffold. Cell 155:1233–1243. https://doi.org/10.1016/j.cell.2013.10.055 PubMedCrossRefGoogle Scholar
  91. 91.
    Shi Y, Fernandez-Martinez J, Tjioe E et al (2014) Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. Mol Cell Proteomics 13:2927–2943. https://doi.org/10.1074/mcp.M114.041673 PubMedPubMedCentralCrossRefGoogle Scholar
  92. 92.
    Oeffinger M (2012) Two steps forward-one step back: advances in affinity purification mass spectrometry of macromolecular complexes. Proteomics 12:1591–1608. https://doi.org/10.1002/pmic.201100509 PubMedCrossRefGoogle Scholar
  93. 93.
    Morris JH, Knudsen GM, Verschueren E et al (2014) Affinity purification–mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc 9:2539–2554. https://doi.org/10.1038/nprot.2014.164 PubMedPubMedCentralCrossRefGoogle Scholar
  94. 94.
    Aebersold R, Mann M (2016) Mass-spectrometric exploration of proteome structure and function. Nature 537:347–355. https://doi.org/10.1038/nature19949 PubMedCrossRefGoogle Scholar
  95. 95.
    Malovannaya A, Lanz RB, Jung SY et al (2011) Analysis of the human endogenous coregulator complexome. Cell 145:787–799. https://doi.org/10.1016/j.cell.2011.05.006 PubMedPubMedCentralCrossRefGoogle Scholar
  96. 96.
    Hein MY, Hubner NC, Poser I et al (2015) A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 163:712–723. https://doi.org/10.1016/j.cell.2015.09.053 PubMedCrossRefGoogle Scholar
  97. 97.
    Huttlin EL, Ting L, Bruckner RJ et al (2015) The BioPlex network: a systematic exploration of the human interactome. Cell 162:425–440. https://doi.org/10.1016/j.cell.2015.06.043 PubMedPubMedCentralCrossRefGoogle Scholar
  98. 98.
    Wan C, Borgeson B, Phanse S et al (2015) Panorama of ancient metazoan macromolecular complexes. Nature 525:339–344. https://doi.org/10.1038/nature14877 PubMedPubMedCentralCrossRefGoogle Scholar
  99. 99.
    Rigaut G, Shevchenko A, Rutz B et al (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17:1030–1032. https://doi.org/10.1038/13732 PubMedCrossRefGoogle Scholar
  100. 100.
    Hubner NC, Bird AW, Cox J et al (2010) Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol 189:739–754. https://doi.org/10.1083/jcb.200911091 PubMedPubMedCentralCrossRefGoogle Scholar
  101. 101.
    Selbach M, Mann M (2006) Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK). Nat Methods 3:981–983. https://doi.org/10.1038/nmeth972 PubMedCrossRefGoogle Scholar
  102. 102.
    Perkins JR, Diboun I, Dessailly BH et al (2010) Transient protein-protein interactions: structural, functional, and network properties. Structure 18:1233–1243. https://doi.org/10.1016/j.str.2010.08.007 PubMedCrossRefGoogle Scholar
  103. 103.
    Keilhauer EC, Hein MY, Mann M (2015) Accurate protein complex retrieval by affinity enrichment mass spectrometry (AE-MS) rather than affinity purification mass spectrometry (AP-MS). Mol Cell Proteomics 14:120–135. https://doi.org/10.1074/mcp.M114.041012 PubMedCrossRefGoogle Scholar
  104. 104.
    Ong S-E, Blagoev B, Kratchmarova I et al (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1(5):376–386. https://doi.org/10.1074/mcp.M200025-MCP200 PubMedCrossRefGoogle Scholar
  105. 105.
    Ross PL (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3:1154–1169. https://doi.org/10.1074/mcp.M400129-MCP200 PubMedCrossRefGoogle Scholar
  106. 106.
    Gygi SP, Rist B, Gerber SA et al (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994–999. https://doi.org/10.1038/13690 PubMedCrossRefGoogle Scholar
  107. 107.
    Thompson A, Schäfer J, Kuhn K et al (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75:1895–1904. https://doi.org/10.1021/ac0262560 PubMedCrossRefGoogle Scholar
  108. 108.
    Liu H, Sadygov RG, Yates JR (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76:4193–4201. https://doi.org/10.1021/ac0498563 PubMedCrossRefGoogle Scholar
  109. 109.
    Zybailov B, Coleman MK, Florens L, Washburn MP (2005) Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem 77:6218–6224. https://doi.org/10.1021/ac050846r PubMedCrossRefGoogle Scholar
  110. 110.
    Lundgren DH, Hwang S-I, Wu L, Han DK (2010) Role of spectral counting in quantitative proteomics. Expert Rev Proteomics 7:39–53. https://doi.org/10.1586/epr.09.69 PubMedCrossRefGoogle Scholar
  111. 111.
    Nahnsen S, Bielow C, Reinert K, Kohlbacher O (2013) Tools for label-free peptide quantification. Mol Cell Proteomics 12:549–556. https://doi.org/10.1074/mcp.R112.025163 PubMedCrossRefGoogle Scholar
  112. 112.
    Fabre B, Lambour T, Bouyssié D et al (2014) Comparison of label-free quantification methods for the determination of protein complexes subunits stoichiometry. EuPA Open Proteom 4:82–86. https://doi.org/10.1016/j.euprot.2014.06.001 CrossRefGoogle Scholar
  113. 113.
    Cox J, Hein MY, Luber CA et al (2014) Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics 13:2513–2526. https://doi.org/10.1074/mcp.M113.031591 PubMedPubMedCentralCrossRefGoogle Scholar
  114. 114.
    Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26:1367–1372. https://doi.org/10.1038/nbt.1511 PubMedCrossRefGoogle Scholar
  115. 115.
    Mertens HDT, Svergun DI (2010) Structural characterization of proteins and complexes using small-angle X-ray solution scattering. J Struct Biol 172:128–141. https://doi.org/10.1016/j.jsb.2010.06.012 PubMedCrossRefGoogle Scholar
  116. 116.
    Zhang Z, Vachet RW (2015) Kinetics of protein complex dissociation studied by hydrogen/deuterium exchange and mass spectrometry. Anal Chem 87:11777–11783. https://doi.org/10.1021/acs.analchem.5b03123 PubMedPubMedCentralCrossRefGoogle Scholar
  117. 117.
    Bernecky C, Herzog F, Baumeister W et al (2016) Structure of transcribing mammalian RNA polymerase II. Nature 529:551–554. https://doi.org/10.1038/nature16482 PubMedCrossRefGoogle Scholar
  118. 118.
    Fernandez-Martinez J, Kim SJ, Shi Y et al (2016) Structure and function of the nuclear pore complex cytoplasmic mRNA export platform. Cell 167:1215–1228.e25. https://doi.org/10.1016/j.cell.2016.10.028 PubMedPubMedCentralCrossRefGoogle Scholar
  119. 119.
    Tsai K-L, Yu X, Gopalan S et al (2017) Mediator structure and rearrangements required for holoenzyme formation. Nature 544:196–201. https://doi.org/10.1038/nature21393 PubMedCrossRefGoogle Scholar
  120. 120.
    Cassiday L (2014) Structural biology: more than a crystallographer. Nature 505:711–713. https://doi.org/10.1038/nj7485-711a PubMedCrossRefGoogle Scholar
  121. 121.
    Appolaire A, Girard E, Colombo M et al (2014) Small-angle neutron scattering reveals the assembly mode and oligomeric architecture of TET, a large, dodecameric aminopeptidase. Acta Crystallogr D Biol Crystallogr 70:2983–2993. https://doi.org/10.1107/S1399004714018446 PubMedPubMedCentralCrossRefGoogle Scholar
  122. 122.
    Macek P, Kerfah R, Erba EB et al (2017) Unraveling self-assembly pathways of the 468-kDa proteolytic machine TET2. Sci Adv 3:e1601601PubMedPubMedCentralCrossRefGoogle Scholar
  123. 123.
    Mallik S, Kundu S (2017) Coevolutionary constraints in the sequence-space of macromolecular complexes reflect their self-assembly pathways. Proteins 85:1183–1189. https://doi.org/10.1002/prot.25292 PubMedCrossRefGoogle Scholar
  124. 124.
    Wilhelm M, Schlegl J, Hahne H et al (2014) Mass-spectrometry-based draft of the human proteome. Nature 509:582–587. https://doi.org/10.1038/nature13319 PubMedCrossRefGoogle Scholar
  125. 125.
    Ezkurdia I, Vázquez J, Valencia A, Tress M (2014) Analyzing the first drafts of the human proteome. J Proteome Res 13:3854–3855. https://doi.org/10.1021/pr500572z PubMedPubMedCentralCrossRefGoogle Scholar
  126. 126.
    Macaulay IC, Ponting CP, Voet T (2017) Single-cell multiomics: multiple measurements from single cells. Trends Genet 33:155–168. https://doi.org/10.1016/j.tig.2016.12.003 PubMedPubMedCentralCrossRefGoogle Scholar
  127. 127.
    Chen S, Wu J, Lu Y et al (2016) Structural basis for dynamic regulation of the human 26S proteasome. Proc Natl Acad Sci U S A 113:12991–12996. https://doi.org/10.1073/pnas.1614614113 PubMedPubMedCentralCrossRefGoogle Scholar

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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.MRC Human Genetics Unit, Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUK

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