Direct correlation of the crystal structure of proteins with the maximum positive and negative charge states of gaseous protein ions produced by electrospray ionization

Journal of the American Society for Mass Spectrometry

Volumn 16, Issue 9, 2005, Pages 1409-1421

  Prakash, Halan ^a   Mazumdar, Shyamalava ^a  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ACIDIC GROUPS; CHARGE STATE; ELECTROSPRAY IONIZATION; ELECTROSPRAY MASS SPECTRUM;

CRYSTAL STRUCTURE; HYDROGEN BONDS; IONIZATION; PROTEINS; SOLUTIONS;

MASS SPECTROMETRY;

CARBONATE DEHYDRATASE; CYTOCHROME C; LYSOZYME; MYOGLOBIN;

ACIDITY; AQUEOUS SOLUTION; ARTICLE; CORRELATION ANALYSIS; CRYSTAL STRUCTURE; ELECTRIC POTENTIAL; ELECTROSPRAY MASS SPECTROMETRY; GAS; HYDROGEN BOND; MOLECULAR INTERACTION; PROTEIN FOLDING; PROTEIN STRUCTURE; SURFACE PROPERTY;

COMPUTER SIMULATION; CRYSTALLOGRAPHY; ELECTROSTATICS; GASES; IONS; MODELS, CHEMICAL; MODELS, MOLECULAR; PHASE TRANSITION; PROTEIN CONFORMATION; PROTEINS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; STATIC ELECTRICITY; STATISTICS; STATISTICS AS TOPIC;

EID: 23844469161     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2005.04.002     Document Type: Article

References (57)

1. S. Cristoni, L.R. Bernardi Development of New Methodologies for the Mass Spectrometry Study of Bioorganic Macromolecules Mass. Spectrom. Rev. 22 2003 369 406
2. J.A. Loo Studying Noncovalent Protein Complexes by Electrospray Ionization Mass Spectrometry Mass. Spectrom. Rev. 16 1997 1 23
3. R.R. Julian, R. Hodyss, J.L. Beauchamp Salt Bridge Stabilization of Charged Zwitterionic Arginine Aggregates in the Gas Phase J. Am. Chem. Soc. 123 2001 3577 3583
4. G. Bouchoux, J.Y. Salpin Gas-Phase Basicity of Glycine, Alanine, Proline, Serine, Lysine, Histidine, and Some of Their Peptides by the Thermokinetic Method Eur. J Mass. Spectrom. (Chichester Eng.) 9 2003 391 402
5. W.I. Burkitt, P.J. Derrick, D. Lafitte, I. Bronstein Protein-Ligand and Protein-Protein Interactions Studied by Electrospray Ionization and Mass Spectrometry Biochem. Soc. Trans. 31 2003 985 989
6. J.M. Wells, P.A. Chrisman, S.A. McLuckey Formation and Characterization of Protein-Protein Complexes In Vacuo J. Am. Chem. Soc. 125 2003 7238 7249
7. D. Lafitte, A.J. Heck, T.J. Hill, K. Jumel, S.E. Harding, P.J. Derrick Evidence of Noncovalent Dimerization of Calmodulin Eur. J. Biochem. 261 1999 337 344
8. R. Daneshfar, E.N. Kitova, J.S. Klassen Determination of Protein-Ligand Association Thermochemistry Using Variable-Temperature Nanoelectrospray Mass Spectrometry J. Am. Chem. Soc. 126 2004 4786 4787
9. R. Grandori Detecting Equilibrium Cytochrome c Folding Intermediates by Electrospray Ionisation Mass Spectrometry Two Partially Folded Forms Populate the Molten-Globule State Protein Sci. 11 2002 453 458
10. L. Konermann, D.J. Douglas Acid-Induced Unfolding of Cytochrome c at Different Methanol Concentrations Electrospray Ionization Mass Spectrometry Specifically Monitors Changes in the Tertiary Structure Biochemistry 36 1997 12296 12302
11. L. Konermann, D.J. Douglas Unfolding of Proteins Monitored by Electrospray Ionization Mass Spectrometry A Comparison of Positive and Negative Ion Modes J. Am. Soc. Mass. Spectrom. 9 1998 1248 1254
12. L. Konermann, D.A. Simmons Protein-Folding Kinetics and Mechanisms Studied by Pulse-Labeling and Mass Spectrometry Mass. Spectrom. Rev. 22 2003 1 26
13. D.A. Simmons, S.D. Dunn, L. Konermann Conformational Dynamics of Partially Denatured Myoglobin Studied by Time-Resolved Electrospray Mass Spectrometry with Online Hydrogen-Deuterium Exchange Biochemistry 42 2003 5896 5905
14. A.T. Iavarone, E.R. Williams Mechanism of Charging and Supercharging Molecules in Electrospray Ionization J. Am. Chem. Soc. 125 2003 2319 2327
15. K.R. Babu, D.J. Douglas Methanol-Induced Conformations of Myoglobin at pH 4.0 Biochemistry 39 2000 14702 14710
16. E.N. Kitova, W. Wang, D.R. Bundle, J.S. Klassen Retention of Bioactive Ligand Conformation in a Gaseous Protein-Trisaccharide Complex J. Am. Chem. Soc. 124 2002 13980 13981
17. S. Zhang, C.K. Van Pelt, D.B. Wilson Quantitative Determination of Noncovalent Binding Interactions Using Automated Nanoelectrospray Mass Spectrometry Anal. Chem. 75 2003 3010 3018
18. S. Wendt, G. McCombie, J. Daniel, A. Kienhofer, D. Hilvert, R. Zenobi Quantitative Evaluation of Noncovalent Chorismate Mutase-Inhibitor Binding by ESI-MS J. Am. Soc. Mass. Spectrom. 14 2003 1470 1476
19. A. Tjernberg, S. Carno, F. Oliv, K. Benkestock, P.O. Edlund, W.J. Griffiths, D. Hallen Determination of Dissociation Constants for Protein-Ligand Complexes by Electrospray Ionization Mass Spectrometry Anal. Chem. 76 2004 4325 4331
20. N. Hagan, D. Fabris Direct Mass Spectrometric Determination of the Stoichiometry and Binding Affinity of the Complexes Between Nucleocapsid Protein and RNA Stem-Loop Hairpins of the HIV-1 Psi-Recognition Element Biochemistry 42 2003 10736 10745
21. A. Kapur, J.L. Beck, S.E. Brown, N.E. Dixon, M.M. Sheil Use of Electrospray Ionization Mass Spectrometry to Study Binding Interactions Between a Replication Terminator Protein and DNA Protein Sci. 11 2002 147 157
22. E.C. Kempen, J.S. Brodbelt A Method for the Determination of Binding Constants by Electrospray Ionization Mass Spectrometry Anal. Chem. 72 2000 5411 5416
23. K. Breuker, H. Oh, D.M. Horn, B.A. Cerda, F.W. McLafferty Detailed Unfolding and Folding of Gaseous Ubiquitin Ions Characterized by Electron Capture Dissociation J. Am. Chem. Soc. 124 2002 6407 6420
24. J.A. Loo Electrospray Ionization Mass Spectrometry A Technology for Studying Noncovalent Macromolecular Complexes Int. J. of. Mass. Spectrom. 200 2000 175 186
25. B. Gologan, Z. Takats, J. Alvarez, J.M. Wiseman, N. Talaty, Z. Ouyang, R.G. Cooks Ion Soft-Landing into Liquids Protein Identification, separation, and Purification with Retention of Biological Activity J. Am. Soc. Mass Spectrom. 15 2004 1874 1884
26. D.S. Gross, P.D. Schnier, S.E. Rodriguez-Cruz, C.K. Fagerquist, E.R. Williams Conformations and Folding of Lysozyme Ions In Vacuo Proc. Natl. Acad. Sci. U.S.A. 93 1996 3143 3148
27. H. Oh, K. Breuker, S.K. Sze, Y. Ge, B.K. Carpenter, F.W. McLafferty 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. N. Felitsyn, M. Peschke, P. Kebarle Origin and Number of Charges Observed on Multiply Protonated Native Proteins Produced by ESI Int. J. Mass Spectrom. 219 2002 39 62
29. J. Fernandez de la Mora Electrospray Ionization of Large Multiply Charged Species Proceeds via Dole's Charged Residue Mechanism Anal. Chim. Acta. 406 2000 93 104
30. P.D. Schnier, D.S. Gross, E.R. Williams On the Maximum Charge State and Proton Transfer Reactivity of Peptide and Protein Ions Formed by Electrospray Ionization J. Am. Soc. Mass Spectrom. 6 1995 1086 1097
31. P. Kebarle A Brief Overview of the Present Status of the Mechanisms Involved in Electrospray Mass Spectrometry J. Mass. Spectrom. 35 2000 804 817
32. V.J. Nesatyy, M.J.-F. Suter On the Conformation-Dependent Neutralization Theory and Charging of Individual Proteins and Their Non-Covalent Complexes in the Gas Phase J. Mass Spectrom. 39 2004 93 97
33. J.C. Jurchen, R.E. Cooper, E.R. Williams The role of acidic residues and of sodium ion adduction on the gas-phase H/D exchange of peptides and peptide dimers J Am. Soc. Mass. Spectrom. 14 12 2003 1477 1487
34. M. Peschke, A. Blades, P. Kebarle Charged States of Proteins. Reactions of Doubly Protonated Alkyldiamines with NH(3): Solvation or Deprotonation. Extension of Two Proton Cases to Multiply Protonated Globular Proteins Observed in the Gas Phase J. Am. Chem. Soc. 124 2002 11519 11530
35. E.R. Williams Proton Transfer Reactivity of Large Multiply Charged ions J. Mass Spectrom. 31 1996 831 842
36. A. Blades, M. Peschke, U. Verkerk, P. Kebarle Rates of Proton Transfer from Carboxylic Acids to Dianions, CO2(CH2)pCO22-, and Their Significance to Observed Negative Charge States of Proteins in the Gas Phase J. Phys. Chem. A 106 2002 10037 10042
37. R. Grandori Origin of the Conformation Dependence of Protein Charge-State Distributions in Electrospray Ionization Mass Spectrometry J. Mass Spectrom. 38 2003 11 15
38. U.H. Verkerk, M. Peschke, P. Kebarle Effect of Buffer Cations and of H3O+ on the Charge States of Native Proteins. Significance to Determinations of Stability Constants of Protein Complexes J. Mass Spectrom. 38 2003 618 631
39. M. Samalikova, I. Matecko, N. Muller, R. Grandori Interpreting Conformational Effects in Protein Nano-ESI-MS Spectra Anal. Bioanal. Chem. 378 2004 1112 1123
40. R. Rodriguez, G. Chinea, N. Lopez, T. Pons, G. Vriend Homology Modeling, Model, and Software Evaluation Three Related Resources 14 1998 523 528
41. G. Vriend WHAT IF A molecular modeling and drug design program J. Mol. Graph. 8 1990 52 56
42. S. Kumar, R. Nussinov Relationship Between Ion Pair Geometries and Electrostatic Strengths in Proteins Biophys. J. 83 2002 1595 1612
43. A.T. Iavarone, O.A. Udekwu, E.R. Williams Buffer Loading for Counteracting Metal Salt-Induced Signal Suppression in Electrospray Ionization Anal. Chem. 76 2004 3944 3950
44. K. Chattopadhyay, S. Mazumdar Stabilization of Partially Folded States of Cytochrome c in Aqueous Surfactant Effects of Ionic and Hydrophobic Interactions Biochemistry 42 2003 14606 14613
45. Z. Zhang, 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 1998 225 233
46. J.L. Stephenson Jr, S.A. McLuckey Ion/Ion Proton Transfer Reactions for Protein Mixture Analysis Anal. Chem. 68 1996 4026 4032
47. M. Samalikova, R. Grandori Role of Opposite Charges in Protein Electrospray Ionization Mass Spectrometry J. Mass Spectrom. 38 2003 941 947
48. M. Hautreux, N. Hue, A. Du Fou. de Kerdaniel, A. Zahir, V. Malec, O. Laprevote Under Non-Denaturing Solvent Conditions, the Mean Charge State of a Multiply Charged Protein Ion Formed by Electrospray Is Linearly Correlated with the Macromolecular Surface Int. J. Mass Spectrom. 231 2004 131 137
49. S.S. Ray, S.K. Singh, P. Balaram An Electrospray Ionization Mass Spectrometry Investigation of 1-Anilino-8-Naphthalene-Sulfonate (ANS) Binding to Proteins J. Am. Soc. Mass Spectrom. 12 2001 428 438
50. A.T. Iavarone, E.R. Williams Supercharging in Electrospray Ionization Effects on Signal and Charge Int. J. Mass Spectrom. 219 2002 63 72
51. O.O. Sogbein, D.A. Simmons, L. Konermann Effects of pH on the Kinetic Reaction Mechanism of Myoglobin Unfolding Studied by Time-Resolved Electrospray Ionization Mass Spectrometry J. Am. Soc. Mass Spectrom. 11 2000 312 319
52. M. Samalikova, R. Grandori Protein Charge-State Distributions in Electrospray-Ionization Mass Spectrometry Do Not Appear to be Limited by the Surface Tension of the Solvent J. Am. Chem. Soc. 125 2003 13352 13353
53. C.V. Robinson, E.W. Chung, B.B. Kragelund, J. Knudsen, R.T. Aplin, F.M. Poulsen, C.M. Dobson Probing the Nature of Noncovalent Interactions by Mass Spectrometry. A Study of Protein-CoA Ligand Binding and Assembly J. Am. Chem. Soc. 118 1996 8646 8653
54. J.A. Loo, P. Hu, P. McConnell, W.T. Muller, S.T. K., V. Thanabal A Study of Src SH2 Domain Protein-Phosphopetide Binding Interactions by Electrospray Ionisation Mass Spectrometry J. Am. Soc. Mass Spectrom. 8 1997 234 243
55. N. Potier, L.J. Donald, I. Chernushevich, A. Ayed, W. Ens, C.H. Arrowsmith, K.G. Standing, H.W. Duckworth Study of a Noncovalent trp Repressor DNA Operator Complex by Electrospray Ionization Time-Of-Flight Mass Spectrometry Protein Sci. 7 1998 1388 1395
56. K.R. Babu, A. Moradian, D.J. Douglas The Methanol-Induced Conformational Transitions of Beta-Lactoglobulin, Cytochrome c, and Ubiquitin at Low pH A Study by Electrospray Ionization Mass Spectrometry J. Am. Soc. Mass Spectrom. 12 2001 317 328
57. D.R. Gumerov, I.A. Kaltashov Dynamics of Iron Release from Transferrin N-lobe Studied by Electrospray Ionization Mass Spectrometry Anal. Chem. 73 2001 2565 2570