Chemical cross-linking and mass spectrometry as structure determination tools

European Journal of Mass Spectrometry

Volumn 13, Issue 2, 2007, Pages 105-113

  Novak, Petr ^a   Giannakopulos, Anastassios E ^b  

^a INSTITUTE OF MICROBIOLOGY   (Czech Republic)

^b UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

Bottom up; Cross linking; FT ICR; High order structure; Mass spectrometry; Protein; Top down

Indexed keywords

CROSS LINKING REAGENT; PROTEIN;

ANIMAL; ARTICLE; CHEMISTRY; ELECTROSPRAY MASS SPECTROMETRY; HUMAN; INFRARED SPECTROSCOPY; METHODOLOGY; PROTEIN CONFORMATION;

ANIMALS; CROSS-LINKING REAGENTS; HUMANS; PROTEIN CONFORMATION; PROTEINS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SPECTROSCOPY, FOURIER TRANSFORM INFRARED;

EID: 34447538183     PISSN: 14690667     EISSN: None     Source Type: Journal    
DOI: 10.1255/ejms.868     Document Type: Article

References (60)

1. "A physical map of the human genome", Nature 409, 934-940 (2001). doi: 10.1038/35057157
2. G.M. Rubin, "The draft sequences-Comparing species", Nature 409, 820-821 (2001). doi: 10.1038/35057277
3. G.A. Wray, M.W. Hahn, E. Abouheif, J.P. Balhoff, M. Pizer, M.V. Rockman and L.A. Romano, "The Evolution of Transcriptional Regulation in Eukaryotes", Mol. Biol. Evol. 20, 1377-1419 (2003). doi: 10.1093/molbev/msg140
4. A.C. Gavin, M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J.M. Rick, A.M. Michon, C.M. Cruciat, M. Remor, C. Höfert, M. Schelder, M. Brajenovic, H. Ruffner, A. Merino, K. Klein, M. Hudak, D. Dickson, T. Rudi, V. Gnau, A. Bauch, S. Bastuck, B. Huhse, C. Leutwein, M.-A. Heurtier, R.R. Copley, A. Edelmann, E. Querfurth, V. Rybin, G. Drewes, M. Raida, T. Bouwmeester, P. Bork, B. Seraphin, B. Kuster, G. Neubauer and G. Superti-Furga, "Functional organization of the yeast proteome by systematic analysis of protein complexes", Nature 415, 141-147 (2002). doi: 10.1038/415141a
5. B. Alberts, "The cell as a collection of protein machines: preparing the next generation of molecular biologists", Cell 92, 291-294 (1998). doi: 10.1016/S0092-8674(00)80922-8
6. V. Ramakrishnan and P.B Moore, "Atomic structures at last: the ribosome in 2000", Curr. Opin. Struct. Biol. 11, 144-154 (2001). doi: 10.1016/S0959-440X(00)00184-6
7. G.M. Clore and A.M. Gronenborn, "NMR structure determination of proteins and protein complexes larger than 20kDa", Curr. Opin. Chem. Biol. 2, 564-570 (1998). doi: 10.1016/81367-5931(98)80084-7
8. D. Staunton, J. Owen and I.D. Campbell "NMR and structural genomics" Acc. Chem. Res. 36, 207-214, (2003). doi: 10.1021/ar010119s
9. W. Jahnke and H. Widmer, "Protein NMR in biomedical research", Cell. Mol. Life Sci. 61, 580-599 (2004). doi: 10.1007/s00018-003- 3382-3
10. C.L. Hanson, H. Videler, C. Santos, J.P.G. Ballesta and C.V. Robinson, "Mass Spectrometry of Ribosomes from Saccharomyces cerevisiae", J. Biol. Chem. 279, 42750-42757 (2004). doi: 10.1074/jbc. M405718200
11. B. Bothner and G. Siuzdak, "Electrospray ionization of a whole virus: analyzing mass, structure, and viability", Chem. Biol. Chem. 5, 258-260 (2004). doi: 10.1002/ cbic.200300754
12. J.J. Thomas, B. Bothner, J. Traina, W.H. Benner and G. Siuzdak, "Electrospray ion mobility spectrometry of intact viruses", Spectroscopy 18, 31-36 (2004).
13. J.A. Loo, "Electrospray ionization mass spectrometry: a technology for studying noncovalent macromolecular complexes", Int. J. Mass Spectrom. 200, 175-186 (2000). doi: 10.1016/S1387-3806(00)00298-0
14. J.M. Daniel, S.D. Friess, S. Rajagopalan, S. Wendt and R. Zenobi, "Quantitative determination of noncovalent binding interactions using soft ionization mass spectrometry", Int. J. Mass Spectrom. 216, 1-27 (2002). doi: 10.1016/S1387-3806(02)00585-7
15. A.J.R. Heck and R.H. van den Heuvel, "Investigation of intact protein complexes by mass spectrometry", Mass Spectrom. Rev. 23, 368-389. (2004). doi: 10.1002/mas.10081
16. C.V. Robinson, "Protein complexes take flight", Nat. Struct. Biol. 9, 505-506 (2002). doi: 10.1038/nsb0702-505
17. F. Sobott and C.V. Robinson, "Protein complexes gain momentum", Curr. Opin. Struct. Biol. 12, 729-734 (2002). doi: 10.1016/S0959-440X(02)00400-1
18. 4 complex in the gas phase: electrospray ionization Fourier transform ion cyclotron resonance", Eur. J. Mass Spectrom. 7, 393-398 (2001).
19. N.B. Gusev, M. Sajgo and P. Friedrich, "Identification of an intra molecular cross-link in tropinin C after cross-linking the proponin complex with 1,3-difluoro-4,6-dinitrobenzene", Biochem. Biophys. Acta 625, 304-309 (1980).
20. K. Yamasaki, N. Sano, M. Ohe and T. Yamamoto, "Determination of the primary structure of intermolecular cross-linking sites on the Ca2+ ATPase of sarcoplasmic reticulum using C14 labeled N-N′(1,4-phenylene)bismalmeide or N-ethylamaleimide", J. Biochem. 108, 918-925 (1990).
21. R. Hartmann-Petersen, K. Tanaka and K.B. Hendil, "Quaternary structure of the ATPase complex of human 26S proteasomes determined by chemical cross-linking.", Arch. Biochem. Biophys. 386, 89-94 (2001). doi: 10.1006/ abbi.2000.2178
22. D.A. Fancy, "Elucidation of protein-protein interactions using chemical cross-linking or label transfer techniques", Curr. Opin. Chem. Biol. 4, 28-33 (2000). doi: 10.1016/S1367-5931(99)00047-2
23. K. Peters and F.M. Richards, "Chemical cross-linking-reagents and problems in studies of membrane structure", Ann. Rev. Biochem. 46, 523-551 (1977). doi: 10.1146/annurev.bi.46.070177.002515
24. J. Brunner, "New photolabelling and cross-linking methods", Ann. Rev. Biochem. 62, 483-514 (1993). doi: 10.1146/annurev.bi.62. 070193.002411
25. D.A. Fancy, "Elucidation of protein-protein interactions using chemical cross-linking or label transfer techniques", Curr. Opin. Chem. Biol. 4, 28-33 (2000). doi: 10.1016/S1367-5931(99)00047-2
26. M.M. Young, N. Tang, J.C. Hempel, C.M. Oshiro, E.W. Taylor, I.D. Kuntz, B.W. Gibson and G. Dollinger," High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry", Proc. Nat. Acad. Sci. USA 97, 5802 (2000). doi: 10.1073/pnas.090099097
27. A. Sinz, "Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes", J. Mass Spectrom. 38, 1225-1237 (2003). doi: 10.1002/jms.559
28. A. Sinz, "Chemical cross-linking and mass spectrometry to map three dimensional protein structures and protein-protein interactions", Mass Spectrom. Rev. 25, 663-682, (2006). doi: 10.1002/mas.20082
29. R. Kluger and A. Alagic, "Chemical cross-linking and protein-protein interactions - A review with illustrative protocols", Bioorg. Chem. 32, 451-472 (2004). doi: 10.1016/j.bioorg.2004.08.002
30. J.W. Back, L. de Jong, A.O. Muijsers and C.G. de Koster, "Chemical cross-linking and mass spectrometry for protein structural modelling", J. Mol. Biol. 331, 303-313 (2003). doi: 10.1016/S0022-2836(03) 00721-6
31. D.M. Schulz, C. Ihling, G.M Clore and A. Sinz, "Mapping the Topology and Determination of a Low-Resolution Three-Dimensional Structure of the Calmodulin-Melittin Complex by Chemical Cross-Linking and High-Resolution FTICRMS: Direct Demonstration of Multiple Binding Modes", Biochemistry 43, 4703-4715 (2004). doi: 10.1021/bi036149f
32. D.R. Müller, P. Schindler, H. Towbin, U. Wirth, H. Voshol, S. Hoving and M.O. Steinmetz, "Isotope-Tagged Cross-Linking Reagents. A New Tool in Mass Spectrometric Protein Interaction Analysis", Anal. Chem. 73, 1927-1934 (2001). doi: 10.1021/ac001379a
33. K.M. Pearson, L.K. Pannell and H.M. Fales, "Intramolecular Cross-Linking Experiments on Cytochrome C and Ribonuclease A Using an Isotope Multiplet Method", Rapid Commun. Mass Spectrom. 16, 149-159 (2002). doi: 10.1002/rcm.554
34. F. Naoaki, R.B. Jacobsen, N.L. Wood, J. Schoeniger and K.R. Guy, "A Novel Protein Crosslinking Reagent for the Determination of Moderate Resolution Protein Structures by Mass Spectrometry (MS3-D)", Bioorg. Med. Chem. Lett. 14, 427-429 (2004). doi: 10.1016/j.bmcl.2003.10.043
35. G. Kruppa, J. Schoeniger and M.M. Young, "A Top Down Approach to Protein Structural Studies Using Chemical Cross-Linking and Fourier Transform Mass Spectrometry", Rapid Commun. Mass Spectrom. 17, 155-162 (2003). doi: 10.1002/rcm.885
36. Z.Q. Zhang and A.G. Marshall, "A universal algorithm for fast and automated charge state deconvolution of electrospray mass-to-charge ratio spectra", J. Am. Soc. Mass Spectrom. 9, 225-233 (1998). doi: 10.1016/S1044-0305(97)00284-5
37. D.M. Horn, R.A. Zubarev and F.W. McLafferty, "Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules", J. Am. Soc. Mass Spectrom. 11, 320-332 (2000). doi: 10.1016/S1044-0305(99)00157-9
38. B. Schilling, R.H. Row, B.W. Gibson, X. Guo and M.M. Young, "MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides", J. Am. Soc. Mass Spectrom. 14, 834-850 (2003). doi: 10.1016/S1044-0305(03)00327-1
39. D.M. Horn, Y. Ge and F.W. McLafferty, "Activated ion electron capture dissociation for mass spectral sequencing of larger (42kDa) proteins", Anal. Chem. 72, 4778-4784 (2000). doi: 10.1021/ac000494i
40. S.D.-H. Shi, M.E. Hemling, S.A. Carr, D.M. Horn, I. Lindh and F.W. McLafferty, "Phosphopeptide/Phosphoprotein Mapping by Electron Capture Dissociation Mass Spectrometry", Anal. Chem. 73, 19-22 (2001). doi: 10.1021/ ac000703z
41. P. Novak, W.E. Haskins, M.J. Ayson, R.B. Jacobsen, J.S. Schoeniger, M.D. Leavell, M.M. Young and G.H. Kruppa, "Unambiguous assignment of intramolecular chemical cross-links in modified mammalian membrane proteins by Fourier transform-tandem mass spectrometry", Anal. Chem. 77, 5101-5106 (2005). doi: 10.1021/ac040194r
42. P. Novak, G.H. Kruppa, M.M. Young and J. Schoeniger, "A Top Down Method for the Determination of Residue Specific Accessibility in Proteins", J. Mass Spectrom., accepted (2003).
43. K.M Pearson, L.K Pannell and H.M. Fales, "Intramolecular cross-linking experiments on cytochrome c and ribonuclease A using an isotope multiplet method", Rapid Commun. Mass Spectrom. 16, 149-159 (2002). doi: 10.1002/rcm.554
44. V. Horneffer, K. Strupata and F. Hillenkamp, "Localization of Noncovalent Complexes in MALD Preparations by CLSM", J. Am. Soc. Mass Spectrom. 17, 1599-1604 (2006). doi: 10.1016/j.jasms.2006.06.028
45. D.C. Schriemer and L. Li, "Detection of high molecular weight narrow polydisperse polymers up to 1.5 million Dallons by MALDI mass spectrometry", Anal. Chem. 68, 2721-2725 (1996). doi: 10.1021/ac960442m
46. M.A. Tito, K. Tars, K. Valegard, J. Hajdu and C.V. Robinson, "Electrospray time-of-flight mass spectrometry of the intact MS2 virus capsid." J. Am. Chem. Soc. 122, 3550-3551 (2000). doi: 10.1021/ja993740k
47. R.J. Wenzel, U. Matter, L. Schultheis and R. Zenobi, "Analysis of megadalton ions using cryodetection MALDI time-of-flight mass spectrometry", Anal. Chem. 77, 4329-4337 (2005). doi: 10.1021/ac0482054
48. A.J. Heck and R.H. Van Den Heuvel, "Investigation of intact protein complexes by mass spectrometry", Mass Spectrom. Rev. 23, 368-389 (2004). doi: 10.1002/mas.10081
49. K. Håkansson, J. Axelsson, M. Palmblad and P. Håkansson, "Mechanistic Studies of Multipole Storage Assisted Dissociation", J. Am. Soc. Mass Spectrom. 11, 210-217, (2000). doi: 10.1016/S1044-0305(99)00144-0
50. L.A. McDonnell, A.E. Giannakopulos, Y.O. Tsybin, P. Håkansson and P.J. Derrick, "A theoretical investigation of the kinetic energy of ions trapped in a radio-frequency hexapole ion trap", Eur. J. Mass Spectrom., 8, 181 (2002). doi: 10.1255/ejms.488
51. E. De Leeuwa, I. Porcellia, F. Sargenta, T. Palmera and B.C. Berksa, "Membrane interactions and self-association of the TatA and TatB components of the twin-arginine translocation pathway", FEBS Lett. 506, 143-148 (2001). doi: 10.1016/ S0014-5793(01)02904-0
52. P. Novak, M.M. Young, J.S. Schoeniger and G.H. Kruppa, "A top-down approach to protein structure studies using chemical cross-linking and Fourier transform mass spectrometry", Eur. J. Mass Spectrom. 9, 623-631 (2003). doi: 10.1255/ejms.590
53. R.B. Jacobsen, K.L. Sale, M.J. Ayson, P. Novak, J. Hong, P. Lane, N.L. Wood, G.H. Kruppa, M.M. Young and J.S. Schoeniger, "Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry", Protein Sci. 15, 1303-1317 (2006). doi: 10.1110/ps.052040406
54. A. Laio and M. Parrinello, "Escaping free-energy minima", PNAS 99, 12562-12566 (2002). doi: 10.1073/pnas.202427399
55. A. Barducci, R. Chelli, P. Procacci, V. Schettino, F.L. Gervasio and M. Parrinello, "Metadynamics Simulation of Prion Protein: a-Structure Stability and the Early Stages of Misfolding", J. Am. Chem. Soc. 128, 2705-2710 (2006). doi: 10.1021/ja0570761
56. J. Gsponer, P. Ferrara and A. Caflisch, "Flexibility of the murine prion protein and its Asp178Asn mutant investigated by molecular dynamics simulations", J. Mol. Graphics Modell. 20, 169-182 (2001). doi: 10.1016/S1093-3263(01)00117-6
57. F. Wang, W. Li, M.R. Emmett, C.L. Hendrickson and A.G. Marshall, "Conformational and Dynamic Changes of Yersinia Protein Tyrosine Phosphatase Induced by Ligand Binding and Active Site Mutation and Revealed by H/D Exchange and Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry", Biochemistry 37, 15289-15299 (1998). doi: 10.1021/bi981481q
58. Y.-F. Wang, M.-Y. Ho and Y.-P. Ho, "Using mass spectrometry to probe the subtle differences in conformations of several cytochromes c in aqueous and methanol solutions", J. Mass Spectrom. 39, 1523-1530 (2004). doi: 10.1002/jms.757
59. Y. Bai, J.S. Milne, L. Mayne and S.W. Englander, "Primary structure effects on peptide group hydrogen-exchange", Proteins-Structure Function and Genetics 17, 75-86 (1993). doi: 10.1002/prot.340170110
60. T. Kodadek, I. Duroux-Richard and J.C. Bonnafous, "Techniques: Oxidative cross-linking as an emergent tool for the analysis of receptor mediated signalling events", Trends Pharmacol. Sci. 26, 210-217 (2005). doi: 10.1016/ j.tips.2005.02.010