An academic paper authored by Tadashi Ando, Associate Professor at the Department of Applied Electronics, Faculty of Advanced Engineering, and Koji Tamura, Professor at the Department of Biological Science and Technology, Faculty of Advanced Engineering, has been selected as the cover story for the journal "Computation".
Authors
Tadashi Ando, Associate Professor at the Department of Applied Electronics, Faculty of Advanced Engineering, Tokyo University of Science
Koji Tamura, Professor at the Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science
Cover of the Publication
Article Title
Quantum Mechanics/Molecular Mechanics Simulations for Chiral-Selective Aminoacylation: Unraveling the Nature of Life
Abstract
Biological phenomena are chemical reactions that are inherently non-static or "flowing" in nature. Molecular dynamics (MD) is a technique used to calculate the interactions between atoms and analyze the dynamics and energy states of molecules, but it cannot handle chemical reactions involving covalent bond formation and breaking. Quantum mechanics/molecular mechanics (QM/MM) method is a solution to this problem. QM/MM umbrella sampling MD simulations, which include an umbrella sampling technique that can compute free-energy profiles, give us a significant clue about transition states of chemical reactions and their free-energy changes, which are pivotal points in understanding the nature of life.
The authors employed the method to elucidate the mechanisms of chiral-selective aminoacylation of an RNA minihelix, considered to be a primordial form of tRNA. The QM/MM umbrella sampling MD simulation, for the first time, elucidated the full atomistic mechanisms of the "flowing" process of the reaction and indicated that the left-handed amino acid (L-Ala) moiety stabilizes the transition state more than the right-handed amino acid (D-Ala), resulting in L-Ala preference in the aminoacylation reaction in the RNA. The authors present here the results of this application to demonstrate the importance of the QM/MM method.
The QM/MM method not only provides important clues for the elucidation of the origin of homochirality, in which proteins in biological systems are composed exclusively of left-handed amino acids, but also is expected to become a pivotal tool in the analysis of biomolecular reactions, combined with the development of artificial intelligence. The journal selected this article for its cover story given the significance of its findings.
Publication date
December 2, 2024
