TY - JOUR
T1 - Direct Dynamics Simulations of the Thermal Fragmentation of a Protonated Peptide Containing Arginine
AU - Gu, Meng
AU - Zhang, Jiaxu
AU - Hase, William L.
AU - Yang, Li
N1 - Funding Information:
This work is supported by the National Natural Science Foundation of China (nos. 21403047, 21573052, and 51536002), the Natural Science Foundation of Heilongjiang Province of China (no. B2017003), and the Robert A. Welch Foundation under grant no. D-0005.
Publisher Copyright:
© 2020 American Chemical Society.
PY - 2020/1/28
Y1 - 2020/1/28
N2 - Arginine has significant effects on fragmentation patterns of the protonated peptide due to its high basicity guanidine tail. In this article, thermal dissociation of the singly protonated glycine-arginine dipeptide (GR-H+) was investigated by performing direct dynamics simulations at different vibrational temperatures of 2000-3500 K. Fourteen principal fragmentation mechanisms containing side-chain and backbone fragmentation were found and discussed in detail. The mechanism involving partial or complete loss of a guanidino group dominates side-chain fragmentation, while backbone fragmentation mainly involves the three cleavage sites of a1-x1+, a2+-x0, and b1-y1+. Fragmentation patterns for primary dissociation have been compared with experimental results, and the peak that was not identified by the experiment has been assigned by our simulation. Kinetic parameters for GR-H+ unimolecular dissociation may be determined by direct dynamics simulations, which are helpful in exploring the complex biomolecules.
AB - Arginine has significant effects on fragmentation patterns of the protonated peptide due to its high basicity guanidine tail. In this article, thermal dissociation of the singly protonated glycine-arginine dipeptide (GR-H+) was investigated by performing direct dynamics simulations at different vibrational temperatures of 2000-3500 K. Fourteen principal fragmentation mechanisms containing side-chain and backbone fragmentation were found and discussed in detail. The mechanism involving partial or complete loss of a guanidino group dominates side-chain fragmentation, while backbone fragmentation mainly involves the three cleavage sites of a1-x1+, a2+-x0, and b1-y1+. Fragmentation patterns for primary dissociation have been compared with experimental results, and the peak that was not identified by the experiment has been assigned by our simulation. Kinetic parameters for GR-H+ unimolecular dissociation may be determined by direct dynamics simulations, which are helpful in exploring the complex biomolecules.
UR - http://www.scopus.com/inward/record.url?scp=85078174967&partnerID=8YFLogxK
U2 - 10.1021/acsomega.9b03091
DO - 10.1021/acsomega.9b03091
M3 - Article
AN - SCOPUS:85078174967
VL - 5
SP - 1463
EP - 1471
JO - ACS Omega
JF - ACS Omega
SN - 2470-1343
IS - 3
ER -