Electron capture dissociation distinguishes a single D-amino acid in a protein and probes the tertiary structure

Journal of the American Society for Mass Spectrometry

Volumn 15, Issue 7, 2004, Pages 1087-1098

  Adams, Christopher M ^a   Kjeldsen, Frank ^a   Zubarev, Roman A ^a,c   Budnik, Bogdan A ^b   Haselmann, Kim F ^b  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^c UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CHIRAL RECOGNITION; NEUTRAL BOND NETWORK;

AMINO ACIDS; HYDROGEN BONDS; PROTEINS;

MASS SPECTROMETRY;

AMINO ACID; ARGININE; ASPARAGINYLLEUCYLTYROSYLISOLEUCYLGLUTAMINYLTRYPTOPHYLLEUCYLLYSYLASPARTYL GLYCYLGLYCYLPROLYLSERYLSERYLGLYCYLARGINYLPROLYLPROLYLPROLYLSERINE; DEXTRO AMINO ACID; GLUTAMINE; HYDROGEN; ION; PROTEIN; TYROSINE; UNCLASSIFIED DRUG;

AMINO ACID ANALYSIS; AMINO ACID SUBSTITUTION; AMINO TERMINAL SEQUENCE; ARTICLE; CHEMICAL BOND; CHEMICAL INTERACTION; CHIRALITY; DISSOCIATION; ELECTRON CAPTURE DISSOCIATION; ELECTROSPRAY; GAS; HYDROGEN BOND; IONIZATION; MASS SPECTROMETRY; MEASUREMENT; PROBABILITY; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTON TRANSPORT; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; STEREOISOMERISM; STRUCTURE ANALYSIS; TEMPERATURE; VIBRATION;

AMINO ACIDS; CRYSTALLOGRAPHY; ELECTRONS; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; MASS SPECTROMETRY; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 3242687241     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2004.04.026     Document Type: Article

References (64)

1. Fenn J.B., Mann M., Chin Kai Meng S.F.W., Whitehouse C.M. Electrospray Ionization for Mass Spectrometry of Large Biomolecules. Science. 246:1989;64-71
2. Eigen M., de Maeyer L. Relaxation Methods. 1963;895-1054 Interscience, New York, NY
3. Oneil K.T., Degrado W.F. A Thermodynamic Scale for the Helix-Forming Tendencies of the Commonly Occurring Amino-Acids. Science. 250:1990;646-651
4. Pace C.N., Shirley B.A., McNutt M., Gajiwala K. Forces Contributing to the Conformational Stability of Proteins. Faseb J. 10:1996;75-83
5. Sturtevant J.M. The Thermodynamic Effects of Protein Mutations. Curr. Opin. Struct. Biol. 4:1994;69-78
6. Kaltashov I.A., Eyles S.J. Studies of Biomolecular Conformations and Conformational Dynamics by Mass Spectrometry. Mass Spectrom. Rev. 21:2002;37-71
7. Lorenz S.A., Maziarz E.P., Wood T.D. Electrospray Ionization Fourier Transform Mass Spectrometry of Macromolecules The First Decade. Appl. Spectroscop. 53:1999;18A-36A
8. Smith R.D., Loo J.A., Loo R.R.O., Busman M., Udseth H.R. Principles and Practice of Electrospray Ionization-Mass-Spectrometry for Large Polypeptides and Proteins. Mass Spectrom. Rev. 10:1991;359-451
9. Pramanik B.N., Bartner P.L., Mirza U.A., Liu Y., Ganguly A.K. Electrospray Ionization Mass Spectrometry for the Study of Non-Covalent Complexes An Emerging Technology. J. Mass Spectrom. 33:1998;911-920
10. Loo J.A. Electrospray Ionization Mass Spectrometry A Technology for Studying Noncovalent Macromolecular Complexes. Int. J. Mass Spectrom. 200:2000;175-186
11. Miranker A.D. Protein Complexes and Analysis of Their Assembly by Mass Spectrometry. Curr. Opin. Struct. Biol. 10:2000;601-606
12. Sobott, F. Protein Complexes Gain Momentum. Curr. Opin. Struct. Biol. 2002, 12, 729-734
13. Jurchen J.C., Williams E.R. Origin of Asymmetric Charge Partitioning in the Dissociation of Gas-phase Protein Homodimers. J. Am. Chem. Soc. 125:2003;2817-2826
14. McLafferty F.W., Guan Z.Q., Haupts U., Wood T.D., Kelleher N.L. Gaseous Conformational Structures of Cytochrome. C. J Am. Chem. Soc. 120:1998;4732-4740
15. Wood T.D., Chorush R.A., Wampler F.M.I.I.I., Little D.P., O'Connor P.B., McLafferty F.W. Gas-Phase Folding and Unfolding of CytochromeC Cations. Proc. Natl. Acad. Sci. U.S.A. 92:1995;2451-2454
16. Lorenz S.A., Maziarz E.P., Woods T.D. Using Solution Phase Hydrogen/Deuterium (H/D) Exchange to Determine the Origin of Non-Covalent Complexes Observed by Electrospray Ionization Mass Spectrometry In Solution or in Vacuo? J. Am. Soc. Mass Spectrom. 12:2001;795-804
17. Wang F., Freitas M.A., Marshall A.G., Sykes B.D. Gas-Phase Memory of Solution-phase Protein Conformation H/D Exchange and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of the N-terminal Domain of Cardiac Troponin. C. Int. J. Mass Spectrom. 192:1999;319-325
18. Green M.K., Lebrilla C.B. Ion-Molecule Reactions as Probes of Gas-phase Structures of Peptides and Proteins. Mass Spectrom. Rev. 16:1997;53-71
19. Loo R.R.O., Smith R.D. Investigation of the Gas-Phase Structure of Electrosprayed Proteins Using Ion-Molecule Reactions. J. Am. Soc. Mass Spectrom. 5:1994;207-220
20. Iavarone A.T., Williams E.R. Collisionally Activated Dissociation of Supercharged Proteins Formed by Electrospray Ionization. Anal. Chem. 75:2003;4525-4533
21. Laskin J., Futrell J.H. Collisional Activation of Peptide Ions in FT-ICR Mass Spectrometry. Mass Spectrom. Rev. 22:2003;158-181
22. Dufresne C.P., Wood T.D., Hendrickson C.L. High-Resolution Electrospray Ionization Fourier Transform Mass Spectrometry with Infrared Multiphoton Dissociation of Glucokinase from. Bacillus stearothermophilus. J. Am. Soc. Mass Spectrom. 9:1998;1222-1225
23. Charlebois J.P., Patrie S.M., Kelleher N.L. Electron Capture Dissociation and C-13, N-15 Depletion for Deuterium Localization in Intact Proteins After Solution-Phase Exchange. Anal. Chem. 75:2003;3263-3266
24. Kjeldsen F., Haselmann K.F., Sorensen E.S., Zubarev R.A. Distinguishing of Ile/Leu Amino Acid Residues in the PP3 Protein by (Hot) Electron Capture Dissociation in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal. Chem. 75:2003;1267-1274
25. Szilagyi Z., Drahos L., Vekey K. Conformation of Doubly Protonated Peptides Studied by Charge-Separation Reactions in Mass Spectrometry. J. Mass Spectrom. 32:1997;689-696
26. Haselmann K.F., Jorgensen T.J.D., Budnik B.A., Jensen F., Zubarev R.A. Electron Capture Dissociation of Weakly Bound Polypeptide Polycationic Complexes. Rapid Commun. Mass Spectrom. 16:2002;2260-2265
27. Oh H., Breuker K., Sze S.K., Ge Y., Carpenter B.K., McLafferty F.W. Secondary and Tertiary Structures of Gaseous Protein Ions Characterized by Electron Capture Dissociation Mass Spectrometry and Photofragment Spectroscopy. Proc. Natl. Acad. Sci. U.S.A. 99:2002;15863-15868
28. Breuker K., Oh H.B., Horn D.M., Cerda B.A., McLafferty F.W. Detailed Unfolding and Folding of Gaseous Ubiquitin Ions Characterized by Electron Capture Dissociation. J. Am. Chem. Soc. 124:2002;6407-6420
29. Horn D.M., Breuker K., Frank A.J., McLafferty F.W. Kinetic Intermediates in the Folding of Gaseous Protein Ions Characterized by Electron Capture Dissociation Mass Spectrometry. J. Am. Chem. Soc. 123:2001;9792-9799
30. Budnik B.A., Nielsen M.L., Olsen J.V., Haselmann K.F., Horth P., Haehnel W., Zubarev R.A. Can Relative Cleavage Frequencies in Peptides Provide Additional Sequence Information? Int. J. Mass Spectrom. 219:2002;283-294
31. Cooper, H. J.; Hudgins, R. R.; Håkansson, K.; Marshall, A. G. Characterization of Amino Acid Side Chain Losses in Electron Capture Dissociation. J. Am. Soc. Mass Spectrom. 2002; 13, 241-249
32. Haselmann K.F., Budnik B.A., Kjeldsen F., Polfer N.C., Zubarev R.A. Can the (·-X) Region in Electron Capture Dissociation Provide Reliable Information on Amino Acid Composition of Polypeptides? Eur. J. Mass Spectrom. (8):2002;461-469
33. Cooper, H. J.; Håkansson, K.; Marshall, A. G.; Hudgins, R. R.; Haselmann, K. F.; Kjeldsen, F.; Budnik, B. A.; Polfer, N. C.; Zubarev, R. A. The Diagnostic Value of Amino Acid Side-Chain Losses in Electron Capture Dissociation of Polyepeptides. Comment on: "Can the (Mo-X) Region in Electron Capture Dissociation Provide Reliable Information on Amino Acid Composition of Polypeptides?" Eur. J. Mass Spectrom. 2003, 9, 221-222
34. Meot-Ner M. The Ionic Hydrogen Bond. 2. Intramolecular and Partial Bonds. Protonation of Polyethers, Crown Ethers, and Diketones. J. Am. Chem. Soc. 105:1983;4906-4911
35. Neidigh J.W., Fesinmeyer R.M., Andersen N.H. Designing a 20-Residue Protein. Nat. Struct. Biol. 9:2002;425-430
36. Snow C.D., Zagrovic B., Pande V.S. The Trp Cage Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations. J. Am. Chem. Soc. 124:2002;14548-14549
37. Qiu L.L., Pabit S.A., Roitberg A.E., Hagen S.J. Smaller and Faster The 20-Residue Trp-cage Protein Folds in 4 mu s. J. Am. Chem. Soc. 124:2002;12952-12953
38. Chowdhury S., Lee M.C., Xiong G.M., Duan Y. Ab Initio Folding Simulation of the Trp-cage Mini-Protein Approaches NMR Resolution. J. Mol. Biol. 327:2003;711-717
39. Carnevali P., To'th G. Toubassi, G.; Meshkat S. N. Fast Protein Structure Prediction Using Monte Carlo Simulations with Modal Moves. J. Am. Chem. Soc. 125:2003;14244-14245
40. Schug, A. H. T.; Wenzel, W. Reproducible Protein Folding with the Stochastic Tunneling Method. Phys. Rev. Lett. 2003, 91, Art. No. 158102
41. Barua B., Andersen N.H. Determinants of Miniprotein Stability Can Anything Replace a Buried H-Bonded Trp Sidechain? Lett. Pept. Sci. 8:2001;221-226
42. Krause E., Beyermann M., Dathe M., Rothemund S., Bienert M. Location of an Amphipathic α-Helix in Peptides Using Reversed-Phase HPLC Retention Behavior of D-Amino-Acid Analogs. Anal. Chem. 67:1995;252-258
43. Mitchell J.B. D-Amino Acid Residues in Peptides and Proteins. Proteins: Structure, Function, and Genomics. 50:2003;563-571
44. Haselmann K.F., Budnik B.A., Olsen J.V., Nielsen M.L., Reis C.A., Clausen H., Johnsen A.H., Zubarev R.A. Advantages of External Accumulation for Electron Capture Dissociation in Fourier Transform Mass Spectrometry. Anal. Chem. 73:2001;2998-3005
45. Tsybin Y.O., Hakansson P., Budnik B.A., Haselmann K.F., Kjeldsen F., Gorshkov M., Zubarev R.A. Improved Low-Energy Electron Injection Systems for High Rate Electron Capture Dissociation in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Rapid Commun. Mass Spectrom. 15:2001;1849-1854
46. Boeckmann B., Bairoch A., Apweiler R., Blatter M.C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., Pilbout S., Schneider M. The SWISS-PROT Protein Knowledgebase and Its Supplement TrEMBL in 2003. Nucl. Acids Res. 31:2003;365-370
47. Humphrey W., Dalke A., Schulten K. VMD Visual Molecular Dynamics. J. Mol. Graphics. 14:1996;33
48. Williams E.R. Proton Transfer Reactivity of Large Multiply Charged Ions. J. Mass Spectrom. 31:1996;831-842
49. Zubarev R.A., Haselmann K.F., Budnik B., Kjeldsen F., Jensen F. Towards an Understanding of the Mechanism of Electron-capture Dissociation A Historical Perspective and Modern Ideas. Eur. J. Mass Spectrom. (8):2002;337-349
50. Tsaprailis G., Nair H., Somogyi A., Wysocki V.H., Zhong W.Q., Futrell J.H., Summerfield S.G., Gaskell S.J. Influence of Secondary Structure on the Fragmentation of Protonated Peptides. J. Am. Chem. Soc. 121:1999;5142-5154
51. Kjeldsen F., Haselmann K.F., Budnik B.A., Jensen F., Zubarev R.A. Dissociative Capture of Hot (3-13 eV) Electrons by Polypeptide Polycations An Efficient Process Accompanied by Secondary Fragmentation. Chem. Phys. Lett. 356:2002;201-206
52. Kjelden F., Zubarev R.A. Secondary Losses via ?-Lactam Formation in Hot Electron Capture Dissociation A Missing Link to Complete de Novo Sequencing of Proteins? J. Am. Chem. Soc. 125:2003;6628-6629
53. Polfer N.C. Structural Elucidation of Peptides and Proteins by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. 2003;Thesis, University of Edinburgh, Edinburgh, UK. 95-226
54. Wu L.M., Cooks R.G. Chiral Analysis Using the Kinetic Method with Optimized Fixed Ligands Applications to Some Antibiotics. Anal. Chem. 75:2003;678-684
55. Wu C., Siems W.F., Klasmeier J., Hill H.H. Separation of Isomeric Peptides Using Electrospray Ionization/High-Resolution Ion Mobility Spectrometry. Anal. Chem. 72:2000;391-395
56. Tao W.A., Zhang D.X., Nikolaev E.N., Cooks R.G. Copper(II)-Assisted Enantiomeric Analysis of D,L-Amino acids Using the Kinetic Method Chiral Recognition and Quantification in the Gas Phase. J. Am. Chem. Soc. 122:2000;10598-10609
57. Salem L.C.X., Segal G., Hiberty. C., Minot C., Leforestier C., Sautet P. Chirality Forces. J. Am. Soc. Mass Spectrom. 109:1987;2887-2894
58. Handman M., Curcuruto O. Probing Conformational Changes in Some Proteins by Positive-Ion Electrospray Mass Spectrometry. Rapid Commun. Mass Spectrom. 8:1994;144-147
59. Jarrold M. Unfolding, Refolding, and Hydration of Proteins in the Gas Phase. Acc. Chem. Res. 32:1999;360-367
60. Schnier P.D., Gross D.S., Williams E.R. Electrostatic Forces and Dielectric Polarizability of Multiply Protonated Gas-Phase Cytochrome-C Ions Probed by Ion/Molecule Chemistry. J. Am. Chem. Soc. 117:1995;6747-6757
61. Wu Z., Fenselau C. Proton Affinity of Arginine Measured by the Kinetic Approach. Rapid Commun. Mass Spectrom. 6:1992;403-405
62. McLafferty F.W. Tandem Mass Spectrometry of Large Molecules. McNeal C.J. Mass Spectrometry in the Analysis of Large Molecules. 1986;J. Wiley, New York. 107-120
63. Zubarev R.A., Kelleher N.L., McLafferty F.W. Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process. J. Am. Chem. Soc. 120:1998;3265-3266
64. Adams, C. M.; Orekhov, V.; Zubarev, R. A., unpublished NMR data