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Influence of stereochemistry on proton transfer in protonated tripeptide models

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Abstract

Vectorial proton transfer among carbonyl oxygen atoms was studied in two models of tripeptide via quantum chemical calculations using the hybrid B3LYP functional and the 6-31++G** basis set. Two principal proton transfer pathways were found: a first path involving isomerization of the proton around the double bond of the carbonyl group, and a second based on the large conformational flexibility of the tripeptide model where all carbonyl oxygen atoms cooperate. The latter pathway has a rate-determining step energy barrier that is only around half of that for the first pathway. As conformational flexibility plays a crucial role in second pathway, the effect of attaching methyl groups to the alpha carbon atoms was studied. The results obtained are presented for all four possible stereochemical configurations.

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References

  1. Pelmenschikov V, Blomberg M, Siegbahn P (2002) A theoretical study of the mechanism for peptide hydrolysis by thermolysin. J Biol Inorg Chem 7:284–298

    Article  CAS  Google Scholar 

  2. Rodiquez C, Cunje A, Shoeib T, Chu I, Hopkinson A, Siu K (2000) Solvent-assisted rearrangements between tautomers of protonated peptides. J Phys Chem A 104:5023–5028

    Article  Google Scholar 

  3. Rodriquez C, Cunje A, Shoeib T, Chu I, Hopkinson A, Siu K (2001) Proton migration and tautomerism in protonated triglycine. J Am Chem Soc 123:3006–3012

    Article  CAS  Google Scholar 

  4. Paizs B, Suhai S (2001) Theoretical study of the main fragmentation pathways for protonated glycylglycine. Rapid Commun Mass Spectrom 15:651–663

    Article  CAS  Google Scholar 

  5. Paizs B, Csonka I, Lendvay G, Suhai S (2001) Proton mobility in protonated glycylglycine and N-formylglycylglycinamide: a combined quantum chemical and RKKM study. Rapid Commun Mass Spectrom 15:637–650

    Article  CAS  Google Scholar 

  6. Smith R, Loo J, Barinaga C, Edmonds C, Udseth H (1990) Collisional activation and collision-activated dissociation of large multiply charged polypeptides and proteins produced by electrospray ionization. J Am Soc Mass Spectrom 1:53–65

    Article  CAS  Google Scholar 

  7. Campbell S, Rodgers M, Marzluff E, Beauchamp J (1995) Deuterium exchange reactions as a probe of biomolecule structure. Fundamental studies of cas phase H/D exchange reactions of protonated glycine oligomers with D2O, CD3OD, CD3CO2D, and ND3. J Am Chem Soc 117:12840–12854

    Google Scholar 

  8. Cassady C, Carr S, Zhang K, Chungphillips A (1995) Experimental and ab-initio studies on protonations of alanine and small peptides of alanine and glycine. J Org Chem 60:1704–1712

    Article  CAS  Google Scholar 

  9. Chaudhuri C, Jiang J, Wu C, Wang X, Chang H (2001) Characterization of protonated formamide-containing clusters by infrared spectroscopy and ab initio calculations. II. Hydration of formamide in the gas phase. J Phys Chem A 105:8906–8915

    Google Scholar 

  10. Csonka I, Paizs B, Lendvay G, Suhai S (2000) Proton mobility in protonated peptides: a joint molecular orbital and RRKM study. Rapid Commun Mass Spectrom 14:417–431

    Article  CAS  Google Scholar 

  11. Martin R (2001) In: Sigel A (ed) Probing of proteins by metal Ions and their low-molecular-weight complexes (Metal Ions in Biological Systems, vol 38). CRC Press, Boca Raton, pp 1–23

  12. MacDonald B, Thachuk M (2008) Gas-phase proton-transfer pathways in protonated histidylglycine. Rapid Commun Mass Spectrom 22:2946–2954

    Article  CAS  Google Scholar 

  13. Fu H, Fu A (2007) Theoretical study on the reaction mechanism of proton transfer in alaninamide. J Mol Struct THEOCHEM 818:163–170

    Article  CAS  Google Scholar 

  14. Richard J, Amyes T (2001) Proton transfer at carbon. Curr Opin Chem Biol 5:626–633

    Article  CAS  Google Scholar 

  15. Hur O, Niks D, Casino P, Dunn M (2002) Proton transfers in the beta-reaction catalyzed by tryptophan synthase. Biochemistry 41:9991–10001

    Article  CAS  Google Scholar 

  16. Tomashek J, Brusilow W (2000) Stoichiometry of energy coupling by proton-translocating ATPases: a history of variability. J Bioenerg Biomembr 32:493–500

    Article  CAS  Google Scholar 

  17. Senior A (1990) The proton-translocating atpase of Escherichia coli. Annu Rev Biophys Bioeng 19:7–41

    Google Scholar 

  18. Green MK, Lebrilla CB (1997) Ion-molecule reactions as probes of gas-phase structures of peptides and proteins. Mass Spectrom Rev 16:53–71

    Article  CAS  Google Scholar 

  19. Papayannopoulos I (1995) The interpretation of collision-induced dissociation tandem mass-spectra of peptides. Mass Spectrom Rev 14:49–73

    Article  CAS  Google Scholar 

  20. Barber M, Bordoli R, Sedgwick R, Tyler A (1981) Fast atom bombardment of solids (fab): a new ion-source for mass-spectrometry. J Chem Soc Chem Commun 325–327

  21. Hillenkamp F, Karas M, Beavis R, Chait B (1991) Matrix-assisted laser desorption ionization mass-spectrometry of biopolymers. Anal Chem 63:A1193–A1202

    Article  Google Scholar 

  22. Fenn J, Mann M, Meng C, Wong S, Whitehouse C (1990) Electrospray ionization: principles and practice. Mass Spectrom Rev 9:37–70

    Google Scholar 

  23. Kulhanek P, Schlag E, Koca J (2003) A novel mechanism of proton transfer in protonated peptides. J Am Chem Soc 125:13678–13679

    Article  CAS  Google Scholar 

  24. Kulhanek P, Schlag E, Koca J (2003) Mechanism of proton transfer in short protonated oligopeptides 1N-methylacetamide and N-2-acetyl-N-1-methylglycinamide. J Phys Chem A 107:5789–5797

    Article  CAS  Google Scholar 

  25. Becke A (1993) Density-functional thermochemistry. 3. The role of exact exchange. J Chem Phys 98:5648–5652

    Google Scholar 

  26. Lee C, Yang W, Parr R (1988) Development of the Colle–Salvetti correlation-energy formula into a functional of the electron-density. Phys Rev B 37:785–789

    Google Scholar 

  27. Miehlich B, Savin A, Stoll H, Preuss H (1989) Results obtained with the correlation-energy density functionals of Becke and Lee, Yang and Parr. Chem Phys Lett 157:200–206

    Article  CAS  Google Scholar 

  28. Hehre W, Ditchfie R, Pople J (1972) Self-consistent molecular-orbital methods. 12. Further extensions of Gaussian-type basis sets for use in molecular-orbital studies of organic molecules. J Chem Phys 56:2257–2261

    Google Scholar 

  29. Harihara P, Pople J (1973) Influence of polarization functions on molecular-orbital hydrogenation energies. Theor Chim Acta 28:213–222

    Article  Google Scholar 

  30. Clark T, Chandrasekhar J, Spitznagel G, PvR S (1983) Efficient diffuse function-augmented basis-sets for anion calculations. 3. The 3-21 + G basis set for 1st-row elements, Li-F. J Comput Chem 4:294–301

    Google Scholar 

  31. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA Jr, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Salvador P, Dannenberg JJ, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Baboul AG, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Andres JL, Gonzalez C, Head-Gordon M, Replogle ES, Pople JA (1998) Gaussian 98, revision A.9. Gaussian Inc., Pittsburgh

  32. Ayala P, Schlegel H (1998) Identification and treatment of internal rotation in normal mode vibrational analysis. J Chem Phys 108:2314–2325

    Article  CAS  Google Scholar 

  33. Desiraju G, Steiner T (1999) The weak hydrogen bond in structural chemistry and biology. Oxford University Press, Oxford

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Acknowledgments

The access to the MetaCentrum supercomputing facilities provided under the research intent MSM6383917201 is appreciated. This work was supported by the Ministry of Education of the Czech Republic, under contracts MSM0021622413 and LC06030 (J.K.). The research leading to these results also received funding from the European Community's Seventh Framework Programme under grant agreement no. 205872 (P.K.).

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Authors and Affiliations

  1. Faculty of Science - National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00, Brno, Czech Republic

    Namat Ali Soliman, Petr Kulhánek & Jaroslav Koča

  2. Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00, Brno, Czech Republic

    Petr Kulhánek & Jaroslav Koča

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  1. Namat Ali Soliman
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  2. Petr Kulhánek
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Correspondence to Jaroslav Koča.

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Soliman, N.A., Kulhánek, P. & Koča, J. Influence of stereochemistry on proton transfer in protonated tripeptide models. J Mol Model 18, 871–879 (2012). https://doi.org/10.1007/s00894-011-1116-2

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  • DOI: https://doi.org/10.1007/s00894-011-1116-2

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