Computational studies on the cognate and non-cognate aminoacyl-tRNAs

• Main Authors: Monajemi, H., Abdullah, W.A.T.W., Zain, Sharifuddin Md
• Format: Article
• Published: Faculty of Science, University of Malaya 2011
• Subjects: QD Chemistry
• Online Access: http://eprints.um.edu.my/6068/; http://www.scopus.com/inward/record.url?eid=2-s2.0-80054122918&partnerID=40&md5=cf93825b877dcc9e9576c81900f3d45d

Although kinetic proofreading plays a major role in the fidelity of protein synthesis, it only includes the codon-anticodon interaction without considering the amino acid side chain. It is not known whether the ribosome has a specific interaction with the amino acid side chain or if the correctly charged tRNA behaves in such a way that brings this fidelity to protein synthesis process. To answer this question, we performed some preliminary calculations using numerical analysis on the misacylated tRNAs and compared the results with that of the cognate aminoacyl-tRNAs. Due to the large size of the molecule, we used 2-layered ONIOM (QM/MM) calculations. Interestingly, it was observed that only the initiator tRNA, mat has a specific interaction with the amino acid side chain.