Peptidyl transferase activity of tRNA: a quantum chemical study.
The mechanism of protein synthesis is still unknown due to inability to detect the so-called enzyme "peptidyl transferase" even after elucidation of high-resolution crystal structure of ribosome. We have recently shown by model building and semi-empirical energy calculation that the tRNA molecule at P-site of ribosome may act as peptidyl transferase (Das et al. (1999) J. Theor. Biol. 200, 193-205). We proposed that the tetrahedral intermediate formed from nucleophylic attack of CO of P-site amino-acylated tRNA by NH2 of A-site amino-acylated tRNA is converted to a six-member ring intermediate by conformational change. This ring intermediate produces a free tRNA and a tRNA covalently linked to a peptide. However, energy of the six-member ring intermediate was calculated to be quite high. We show here that the energy values of all the reactants, intermediates and products are within the expected range when they are calculated using high level ab initio quantum chemical methods.
Bhattacharyya
D
D
Biophysics Division, Saha Institute of Nuclear Physics, 37 Belgachia Road, Calcutta 700037, India. bhatta@biop.saha.ernet.in
Das
G K
GK
Burma
D P
DP
D000409:Alanine / Q000737:chemistry; D001665:Binding Sites; D007700:Kinetics; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry*; D010458:Peptidyl Transferases / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D012343:RNA, Transfer / Q000737:chemistry*; D012266:Ribose / Q000737:chemistry; D013816:Thermodynamics
D010455:Peptides; D012266:Ribose; D012343:RNA, Transfer; D010458:Peptidyl Transferases; D000409:Alanine