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A calculation by using semiempirical potentials of a complex of nucleotides and the cognate amino acid: A numerical approach to the amino acid recognition by tRNA for the ten typical cases
Author(s) -
Yoneda Shigetaka
Publication year - 2009
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.560280719
Subject(s) - pseudorotation , nucleotide , amino acid , chemistry , genetic code , transfer rna , amino acid residue , computational chemistry , stereochemistry , molecule , peptide sequence , biochemistry , rna , organic chemistry , gene
Calculations were carried out to examine the conformation of the complex of four nucleotides and the cognate amino acid proposed by Shimizu [1] as the amino acid recognition mechanism of tRNA. The conformation of this complex was determined by varying the torsion angles, the pseudorotation parameters for puckering of riboses, and the relative positions of the nucleotides and the amino acid. The total energy was calculated by using six semiempirical potentials (Lennard‐Jones 6–12 potential, etc.). The conformation of the complex was searched numerically by the energy minimum principle. Calculation was carried out for seven amino acids. Including the previous study for 3 amino acids, the study for the 10 typical cases in the 64 genetic codes gave the detailed conformations and the energetic structures for the above complexes. These calculafional studies explain the genetic code successfully. The conformational change of the C4N's was discussed.