Molecular electric mechanism for discrimination of amino acid by cognate tRNA

Abstract

In previous article [l-31, we pointed out by using the CPK molecular model that the complex of the three anticodon bases and the discriminator base (C4N) on tRNA can discriminate the cognate amino acid by the lock and key relationship. Analysis of the amino acid sequences of the aminoacyl-tRNA-synthetases reveals an electric machine mechanism for the conformational change of tRNA from an L letter shape to a U letter shape, resulting in the formation of C4N in the active =% structure of the synthetase. From this point of view, a possible ancient protein synthesis system has been speculated. The C4N SchemeThe stereochemical hypothesis of the genetic code usually assumes that either codon or anticodon bases have specific interaction with the cognate amino acid. If the assumption is strictly correct, protein could be formed directly on DNA or RNA by aligning an amino acid on every three bases with some help from the skillfully invented enzymes to connect the amino acids. Since the genetic code dictates only the -correspondence (not the direction of information transfer) of codon or anticodon to amino acid, the above synthetic system might have resulted in the nucleic acid synthesis on protein. However, the acquired heredity advocated by Lamarck has hardly been accepted.Consequently, it appears that another factor is necessary to specify the cognate amino acid by nucleotides. We have previously pointed out by model building [l-31 that a complex of four nucleotides (C4N), namely, that of three anticodon bases with the discriminator base at the fourth position of the 3' end of a tRNA, has a pocket to discriminate the cognate amino acid by the lock and key relationship. This scheme can explain [4] (1) how 20 kinds of protein amino acids were selected from more than 300 amino acids, (2) the unique chirality of protein amino acids on the earth, and (3) the central dogma of molecular biology.The central dogma is guaranteed by the whole system of protein synthesis, in particular, the presence of the adaptor, tRNA. In the C4N scheme, the C4N should first be formed in the aminoacylation process to charge the cognate amino acid, but later be