Computation, Volume 12, Issue 12
2024 December - 20 articles
Cover Story: Quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations give us an important clue about the transition states of chemical reactions and their free energy levels. By applying this method to the chiral-selective aminoacylation of an RNA minihelix (primitive form of tRNA), we elucidated, for the first time, the “flowing” atomistic mechanisms of the reaction and showed that the left-handed amino acid (L-alanine) moiety stabilizes the transition state more than the right-handed amino acid (D-alanine), resulting in L-alanine preference in the aminoacylation reaction in the RNA. Our results provided an important clue to the origin of “homochirality”, in which proteins in biological systems are composed exclusively of left-handed amino acids. View this paper - Issues are regarded as officially published after their release is announced to the table of contents alert mailing list .
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