Molecular Dynamics Simulation of a tRNA-Leucine Dimer with an A3243G Heteroplasmy Mutation in Human Mitochondria Using a Secondary Structure Prediction Approach

Abstract

Mitochondrial DNA mutations, such as A3243G, can affect changes in the structure of biomolecules, resulting in changes in the structure of Leucine transfer Ribose Nucleic Acid to form a dimer. Dimer structure modeling is needed to determine the properties of the structure. However, the lack of a structure template for the transfer of Ribose Nucleic Acid (tRNA) is challenging for the modeling of mutant structures of tRNA, especially mitochondrial tRNA that are susceptible to mutation. Therefore, this study predicted the structure of mitochondrial leucine tRNA and its stability through a knowledge-based method and molecular dynamics. Structural modeling and initial assessment were performed using RNAComposer and MolProbity, HNADOCK, and Discovery studios to form the dimer structure. Molecular dynamics simulations for stability analysis were performed using Amber and AmberTools20 software, showing that the conformational energy of the mutant leucine tRNA dimer structure was lower than the native structure. Moreover, the Root Mean Square Deviation (RMSD) of monomer native leucine tRNA was lower than the mutant, indicating that the dimer structure of mutant leucine tRNA is more stable than usual, and the normal leucine tRNA is more stable than the mutant.