Possible mechanisms for protecting N{single bond}Cα bonds in helical peptides from electron-capture (or transfer) dissociation

International Journal of Mass Spectrometry

Volumn 265, Issue 2-3, 2007, Pages 197-212

  Skurski, Piotr ^a   Sobczyk, Monika ^a   Jakowski, Jacek ^b   Simons, Jack ^a  

^a UNIVERSITY OF UTAH   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

Alpha helix; Coulomb stabilization; Electron capture dissociation; Electron transfer dissociation; N single bond C alpha cleavage

Indexed keywords

EID: 34447579006     PISSN: 13873806     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijms.2007.02.001     Document Type: Article

References (55)

1. Zubarev R.A., Kelleher N.L., and McLafferty F.W. J. Am. Chem. Soc. 120 (1998) 3265
2. Zubarev R.A., Kruger N.A., Fridriksson E.K., Lewis M.A., Horn D.M., Carpenter B.K., and McLafferty F.W. J. Am. Chem. Soc. 121 (1999) 2857
3. Zubarev R.A., Horn D.M., Fridriksson E.K., Kelleher N.L., Kruger N.A., Lewis M.A., Carpenter B.K., and McLafferty F.W. Anal. Chem. 72 (2000) 563
4. Zubarev R.A., Haselmann K.F., Budnik B., Kjeldsen F., and Jensen F. Eur. J. Mass Spectrom. 8 (2002) 337
5. Syka J.E.P., Coon J.J., Schroeder M.J., Shabanowitz J., and Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 9523
6. Coon J.J., Syka J.E.P., Schwartz J.C., Shabanowitz J., and Hunt D.F. Inter. J. Mass Spectrom. 236 (2004) 33
7. Pitteri S.J., Chrisman P.A., and McLuckey S.A. Anal. Chem. 77 (2005) 5662
8. Gunawardena H.P., He M., Chrisman P.A., Pitteri S.J., Hogan J.M., Hodges B.D.M., and McLuckey S.A. J. Am. Chem. Soc. 127 (2005) 12627
9. Syrstad E.A., and Turecek F. J. Phys. Chem. A105 (2001) 11144
10. Turecek F., and Syrstad E.A. J. Am. Chem. Soc. 125 (2003) 3353-3369
11. Turecek F., Polasek M., Frank A., and Sadilek M. J. Am. Chem. Soc. 122 (2000) 2361
12. Syrstad E.A., Stephens D.D., and Turecek F. J. Phys. Chem. A107 (2003) 115
13. Turecek F. J. Am. Chem. Soc. 125 (2003) 5954
14. Syrstad E.A., and Turecek F. Am. Soc. Mass Spectrom. 16 (2005) 208
15. Uggerud E. Inter. J. Mass. Spectrom. 234 (2004) 45
16. Anusiewicz I., Berdys-Kochanska J., and Simons J. J. Phys. Chem. A109 (2005) 5801
17. Anusiewicz I., Berdys-Kochanska J., Skurski P., and Simons J. J. Phys. Chem. A110 (2006) 1261
18. Sawicka A., Skurski P., Hudgins R.R., and Simons J. J. Phys. Chem. B107 (2003) 13505
19. Sobczyk M., Skurski P., and Simons J. Adv. Quantum Chem. 48 (2005) 239
20. Sawicka A., Berdys-Kochaska J., Skurski P., and Simons J. Inter. J. Quantum Chem. 102 (2005) 838
21. Anusiewicz I., Berdys J., Sobczyk M., Sawicka A., Skurski P., and Simons J. J. Phys. Chem. A109 (2005) 250
22. Bakken V., Helgaker T., and Uggerud E. Eur. J. Mass Spectrom. 10 (2004) 625
23. +) the positive charge may be somewhat delocalized so a computation of the Coulomb potential using the location of one atom (e.g., the N atom) to define the distance R can be expected to give only a qualitative estimate.
24. Dezarnaud-Dandine C., Bournel F., Troncy M., Jones D., and Modelli A. J. Phys. B: At. Mol. Opt. Phys. 31 (1998) L497
25. Seydou M., Modelli A., Lucas B., Konate K., Desfrancois C., and Schermann J.P. Eur. Phys. J. D 35 (2005) 199
26. Sobczyk M., and Simons J. J. Phys. Chem. B 110 (2006) 7519
27. Sobczyk M., and Simons J. Inter. J. Mass. Spectrom. 253 (2006) 274
28. -2 dependence relates to the fraction of the surface of a sphere of radius R that overlaps the OCN π* or SS σ* orbital a distance R away.
29. When more than one positive site is present, one must use the sum of such factors to evaluate the Coulomb potential.
30. The workers of Ref. [3j] cite the following reference in support of this claim:. Hudgins R.R., and Jarrold M.F. J. Am. Chem. Soc. 121 (1999) 3494 In this paper, a singly-charged anlog of the species shown in Fig. 1 was used and found to display extended rather than compact structure, suggesting that the doubly-charged species would also be extended because it would also have internal Coulomb repulsion between the two positive Lys sites
31. A more recent effort aimed at using mobility measurements to probe extended and more compact structures of alanine-containing peptides is given in:. Counterman A.E., and Clemmer D.E. J. Phys. Chem. B 107 (2003) 2111
32. - methylene units. It might be that the rate of migration along peptide backbones, where both σ and π bonds occur, is significantly faster. We are in the process of considering this possibility at present.
33. -10 or smaller, essentially ruling out the TBET mechanism for the case under discussion. We note that these β parameters are not out of line with what one observes in other through-bond electron transfer processes. See, for example:. McConnell H.M. J. Chem. Phys. 35 (1961) 508
34. Hoffmann R. Acc. Chem. Res. 4 (1971) 1
35. Newton M.D. Inter. J. Quantum Chem. 77 (2000) 255
36. Jordan K.D., and Paddon-Row M.N. Chem. Rev. 92 (1992) 395
37. Paulson B.P., Curtiss L.A., Bal B., Closs G.L., and Miller J.R. J. Am. Chem. Soc. 118 (1996) 378
38. Hudgins R., Håkansson K., Quinn J.P., Hendrickson C.L., and Marshall A.G. Proceedings of the 50th ASMS Conference on Mass Spectrometry and Allied Topics. Orlando, Florida, June 2-6 (2002). A020420. Fig. 1 first appears in publication in Ref. [3j]. In Ref. [9] another depiction of this kind of extended helical structure appears.
39. McLean A.D., and Chandler G.S. J. Chem. Phys. 72 (1980) 5639
40. Krishnan R., Binkley J.S., Seeger R., and Pople J.A. J. Chem. Phys. 72 (1980) 650
41. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Montgomery Jr. J.A., Vreven T., Kudin K.N., Burant J.C., Millam J.M., Iyengar S.S., Tomasi J., Barone V., Mennucci B., Cossi M., Scalmani G., Rega N., Petersson G.A., Nakatsuji H., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Klene M., Li X., Knox J.E., Hratchian H.P., Cross J.B., Bakken V., Adamo C., Jaramillo J., Gomperts R., Stratmann R.E., Yazyev O., Austin A.J., Cammi R., Pomelli C., Ochterski J.W., Ayala P.Y., Morokuma K., Voth G.A., Salvador P., Dannenberg J.J., Zakrzewski V.G., Dapprich S., Daniels A.D., Strain M.C., Farkas O., Malick D.K., Rabuck A.D., Raghavachari K., Foresman J.B., Ortiz J.V., Cui Q., Baboul A.G., Clifford S., Cioslowski J., Stefanov B.B., Liu G., Liashenko A., Piskorz P., Komaromi I., Martin R.L., Fox D.J., Keith T., Al-Laham M.A., Peng C.Y., Nanayakkara A., Challacombe M., Gill P.M.W., Johnson B., Chen W., Wong M.W., Gonzalez C., and Pople J.A. Gaussian 03, Revision A 1 (2004), Gaussian, Inc., Wallingford, CT
42. Schaftenaar G., and Noordik J.H. J. Comput. Aided Mol. Des. 14 (2000) 123
43. See Table 1 in Ref. [3e].
44. Savitski M.M., Kjeldsen F., Nielsen M.L., and Zubarev R.A. J. Am. Soc. Mass. Spectom. 18 (2007) 113
45. Breuker K., Oh H., Lin C., Carpenter B.K., and McLafferty F.W. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 14011
46. Tsybin Y.O., Emmett M.R., Hendrickson C.L., Tsybin O.Y., and Marshall A.G. Am. Soc. Mass Spectrom. (2006) (abstract)
47. Leymarie N., Costello C.E., and O'Connor P.B. J. Am. Chem. Soc. 125 (2003) 8949
48. Tsybin Y.O., Tysbin O.Y., Grigoriev P.D., Emmett M.R., Hendrickson C.L., and Marshall A.G. Inter. Mass Spectrom. Confer. (2006) (abstract)
49. In Ref. [3][3f] it was noted (for the first time to our knowledge) that the electron-attached OCN- moiety has a very high proton affinity (as high as 300 kcal mol-1), so it can abstract a proton from any protonated amino acid residue. However, to abstract a proton from the H{single bond}N backbone bond that belongs to the amino acid to which the electron-attached amino acid is hydrogen bonded requires even more than 310 kcal mol-1. For this reason, the helix-involved electron-attached OCN units remain in the NCO-⋯H{single bond}N state rather than moving to the NCO-H⋯N- state (2000).
50. Horn D.M., Breuker K., Frank A.J., and McLafferty F.W. J. Am. Chem. Soc. 123 (2001) 9792
51. Horn D.M., Ge Y., and McLafferty F.W. Anal. Chem. 72 (2000) 4778
52. Cooper H.J., Håkansson K., and Marshall A.G. Mass Spectrom. Rev. 24 (2005) 201
53. Patriksson A., Adams C., Kjeldsen F., Raber J., van der Spoel D., and Zubarev R.A. Inter. J. Mass Spec. 248 (2006) 124
54. + ion will be minor for amino acids near the C-termini
55. Lin C., Cournoyer J.J., and O'Connor P.B. J. Am. Soc. Mass Spectrom. 17 (2006) 1605