Direct Dynamics Simulations of the Thermal Fragmentation of a Protonated Peptide Containing Arginine.

ABSTRACT: 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 identif

SUBMITTER: Gu M 

PROVIDER: S-EPMC6990424 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature