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The Emergence of New Radical-Cationic Amino Acid Dynamics: The Proton Patches Model

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The Emergence of New Radical-Cationic Amino Acid Dynamics: The Proton Patches Model

  1. 1. The Emergence of a New Radical-Cationic Amino Acid Dynamics: The Proton Patches Model
  2. 2. Where I’m Going With It All • “Proton scissors” • “Proton patches” • Examples and results
  3. 3. Methodology • Lowest energy conformers of neutral amino acid • Geometry in Gaussian • Charge = +1; Multiplicity = 2 (ionization) • Run CPMD simulation to test
  4. 4. “Proton Scissors” 12 AWFULLY COMPLICATED STEPS This fragmentation of C-N bond to give oxazolone cation and neutral fragment occurs at 31.3 kcal/mol. This size barrier is common with protonated species (between 30 and 40 kcal/mol). The fragmentation of any C-N or C-C bond in GGG is always preceded by proton transfer. Fragments + + Rodriquez, C.F.,
  5. 5. Amino Acids • Arginine • Asparigine • Aspartic Acid • Threonine • Tryptophan
  6. 6. Radical-Cationic Arginine (Arg+• )
  7. 7. Arg+• 0 2 4 6 8 10 12 0 100 200 300 400 500 600 700 800 Time (fs) C-CBondLength(Angstroms)
  8. 8. Arg+• 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2 0 100 200 300 400 500 600 700 800 Time (fs) N-HBondDistance(Angstroms)
  9. 9. Radical-Cationic Asparigine (Asn+• )
  10. 10. Asn+• 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2 2.2 0 100 200 300 400 500 600 700 800 Time (fs) O-HBondDistance(Angstroms)
  11. 11. Asn+• 0 1 2 3 4 5 6 7 0 100 200 300 400 500 600 700 800 Time (fs) C-CBondDistance(Angstroms)
  12. 12. Radical-Cationic Aspartic Acid (Asp+• )
  13. 13. Asp+• 0 1 2 3 4 5 6 7 0 100 200 300 400 500 Time (fs) C-CBondDistance(Angstroms)
  14. 14. Asp+• 0 1 2 3 4 5 6 0 100 200 300 400 500 Time (fs) O-HBondDistance
  15. 15. Asp+• 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 0 100 200 300 400 500 Time (fs) O-HBondDistance
  16. 16. Asp+• 0 1 2 3 4 5 6 0 100 200 300 400 500 Time (fs) O-HBondDistance(Angstroms) ~124 fs
  17. 17. Radical-Cationic Threonine (Thr+• )
  18. 18. Thr+• 0 2 4 6 8 10 12 0 100 200 300 400 500 600 700 800 Time (fs) C-CBondLength(Angstroms)
  19. 19. Thr+• (Other conformer) 0 1 2 3 4 5 6 0 100 200 300 400 500 600 Time (fs) C-CBondLength(Angstroms)
  20. 20. Thr+• 0 0.5 1 1.5 2 2.5 3 3.5 0 100 200 300 400 500 600 Time (fs) O-HBondDistance(Angstroms)
  21. 21. Radical-Cationic Tryptophan (Trp+• )
  22. 22. Trp+• 0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 0 100 200 300 400 500 600 700 800 Time (fs) C-CBondLength
  23. 23. Summary • Radical-cationic amino acids do not obey the “proton scissors” motif (Proton transfer before C- C bond cleavage); we see variety • Arg+• , Asp+• , and Thr+• (conformer 2) show C-C bond cleavage before proton transfer • Asn+• shows C-C bond cleavage and proton transfer occurring almost simultaneously • Thr+• , Trp+• show C-C bond cleavage without any proton transfer • Explanation for lack of IE potentials of amino acids
  24. 24. Future Work • Di- and tripeptides (ThrGly, GlyThr, …) • Cu2+ complexes • Cys+• (problems) • GROMACS
  25. 25. Acknowledgements Nicole McNeil Liu Yang James Goodine Dr. Orlova CBU ATCS
  26. 26. Thr+• 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 2 0 100 200 300 400 500 600 Time (fs) O-HBondLength(Angstroms)

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