title: Transfer RNA docking pair model in the ribosomal pre- and post-translocational states.
abstract: A consensus has been reached that the conformation of the anticodon-codon interactions of two adjacent tRNA molecules on the ribosome is a Sundaralingam-type (S-type). Even if it is kept to the S-type, there are still various possibilities. Various experimental data have been supporting an idea that the conformation of A-site tRNA is different from that of P-site tRNA. Those data as well as the recent result of Brimacombe and co-workers that U20:1 of lupin tRNAmMetbound to the A-site was cross-linked to a region, 875-905, of 23S rRNA in combination with the other recent findings of Nierhaus and co-workers about the spin-contrast method of neutron diffraction of the ribosome and the better accessible nucleotide patterns of phosphorothioated tRNAs on the ribosome have led to a new tRNA docking pair model, in which the highly conserved G18 and G19 of D-loop in A-site tRNA and C56 and C61 of TpsiC-loop in P-site tRNA base pair along with the conventional base pairs of adjacent codon-anticodon interactions. This A-P tRNA pair model can be translocated to the P-E tRNA pair model without changing the conformation except the ACCA termini, keeping the position of the growing nascent polypeptide chain.
authors.affiliation: Department of Information Dynamics, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakaecho, Itabashi-ku, Tokyo 173, Japan. knagano@info.ncc.go.jp
authors.forename: K
authors.initials: K
authors.lastname: Nagano
authors.forename: N
authors.initials: N
authors.lastname: Nagano
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D004926:Escherichia coli; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010944:Plants; D012338:RNA, Ribosomal, 23S / Q000737:chemistry*; D012343:RNA, Transfer / Q000737:chemistry*; D012358:RNA, Transfer, Met / Q000737:chemistry; D012362:RNA, Transfer, Ser / Q000737:chemistry; D012270:Ribosomes / Q000378:metabolism*; D012441:Saccharomyces cerevisiae; D012984:Software
chemical_list: D012338:RNA, Ribosomal, 23S; D012358:RNA, Transfer, Met; D012362:RNA, Transfer, Ser; D012343:RNA, Transfer