TY - JOUR
T1 - Thermodynamics and Mechanisms of Protonated Asparaginyl-Glycine Decomposition
AU - Boles, Georgia C.
AU - Wu, R. R.
AU - Rodgers, M. T.
AU - Armentrout, P. B.
N1 - Publisher Copyright:
© 2016 American Chemical Society.
PY - 2016/7/14
Y1 - 2016/7/14
N2 - Deamidation at asparagine residues, a spontaneous post-translational modification in proteins, plays a significant role in various biological processes and degenerative diseases. In the current work, we present a full description of the deamidation process as well as other key fragmentations (dehydration, peptide bond cleavage, and loss of 2 NH3) from protonated asparaginyl-glycine, H+(AsnGly), by studying its kinetic energy dependent collision-induced dissociation (CID) with Xe using a guided ion beam tandem mass spectrometer. These results are compared with those for sustained off-resonance irradiation (SORI)-CID of H+(AsnGly) with Ar in a Fourier transform ion cyclotron resonance mass spectrometer. Computationally, simulating annealing methodology and a series of relaxed potential energy scans at the B3LYP/6-31G(d) level were performed to identify all intermediate and transition state (TS) structures for each key reaction. All species were further optimized at the B3LYP and B3LYP-GD3BJ/6-311+G(d,p) levels of theory. Single point energies of all major reaction species were calculated at the B3LYP, B3P86, MP2(full), and B3LYP-GD3BJ levels of theory and using M06-2X for rate-limiting species. Relative energies of intermediates, TSs, and products allow characterization of the elementary and rate limiting steps in H+(AsnGly) decomposition. By combining experimental and computational results, the complete mechanistic nature of H+(AsnGly) deamidation and other fragmentations is explored and compared to the previously studied H+(Asn) complex. The influence of water solvation on key TSs is also explored. On a fundamental level, this analysis will aid in understanding the thermodynamic and kinetic characteristics of the key intramolecular interactions involved in deamidation, dehydration, and other important fragmentations of peptides.
AB - Deamidation at asparagine residues, a spontaneous post-translational modification in proteins, plays a significant role in various biological processes and degenerative diseases. In the current work, we present a full description of the deamidation process as well as other key fragmentations (dehydration, peptide bond cleavage, and loss of 2 NH3) from protonated asparaginyl-glycine, H+(AsnGly), by studying its kinetic energy dependent collision-induced dissociation (CID) with Xe using a guided ion beam tandem mass spectrometer. These results are compared with those for sustained off-resonance irradiation (SORI)-CID of H+(AsnGly) with Ar in a Fourier transform ion cyclotron resonance mass spectrometer. Computationally, simulating annealing methodology and a series of relaxed potential energy scans at the B3LYP/6-31G(d) level were performed to identify all intermediate and transition state (TS) structures for each key reaction. All species were further optimized at the B3LYP and B3LYP-GD3BJ/6-311+G(d,p) levels of theory. Single point energies of all major reaction species were calculated at the B3LYP, B3P86, MP2(full), and B3LYP-GD3BJ levels of theory and using M06-2X for rate-limiting species. Relative energies of intermediates, TSs, and products allow characterization of the elementary and rate limiting steps in H+(AsnGly) decomposition. By combining experimental and computational results, the complete mechanistic nature of H+(AsnGly) deamidation and other fragmentations is explored and compared to the previously studied H+(Asn) complex. The influence of water solvation on key TSs is also explored. On a fundamental level, this analysis will aid in understanding the thermodynamic and kinetic characteristics of the key intramolecular interactions involved in deamidation, dehydration, and other important fragmentations of peptides.
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U2 - 10.1021/acs.jpcb.6b03253
DO - 10.1021/acs.jpcb.6b03253
M3 - Article
C2 - 27322599
AN - SCOPUS:84978732224
SN - 1520-6106
VL - 120
SP - 6525
EP - 6545
JO - Journal of Physical Chemistry B
JF - Journal of Physical Chemistry B
IS - 27
ER -