title: Identical RNA-protein interactions in vivo and in vitro and a scheme of folding the newly synthesized proteins by ribosomes.
abstract: A distinct three-dimensional shape of rRNA inside the ribosome is required for the peptidyl transfer activity of its peptidyltransferase center (PTC). In contrast, even the in vitro transcribed PTC RNA interacts with unfolded protein(s) at about five sites to let them attain their native states. We found that the same set of conserved nucleotides in the PTC interact identically with nascent and chemically unfolded proteins in vivo and in vitro, respectively. The time course of this interaction, difficult to follow in vivo, was observed in vitro. It suggested nucleation of folding of cytosolic globular proteins vectorially from hydrophilic N to hydrophobic C termini, consistent with our discovery of a regular arrangement of cumulative hydrophobic indices of the peptide segments of cytosolic proteins from N to C termini. Based on this observation, we propose a model here for the nucleation of folding of the nascent protein chain by the PTC.
authors.affiliation: Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, 92-A.P.C. Road, Kolkata 700 009, India.
authors.forename: Debasis
authors.initials: D
authors.lastname: Das
authors.forename: Dibyendu
authors.initials: D
authors.lastname: Samanta
authors.forename: Salman
authors.initials: S
authors.lastname: Hasan
authors.forename: Anindita
authors.initials: A
authors.lastname: Das
authors.forename: Arpita
authors.initials: A
authors.lastname: Bhattacharya
authors.forename: Santanu
authors.initials: S
authors.lastname: Dasgupta
authors.forename: Abhijit
authors.initials: A
authors.lastname: Chakrabarti
authors.forename: Pradip
authors.initials: P
authors.lastname: Ghorai
authors.forename: Chanchal
authors.initials: C
authors.lastname: Das Gupta
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D004926:Escherichia coli / Q000201:enzymology / Q000378:metabolism*; D006801:Humans; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010458:Peptidyl Transferases / Q000378:metabolism; D011485:Protein Binding; D014176:Protein Biosynthesis; D017510:Protein Folding; D055550:Protein Stability; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D054681:Ribosome Subunits, Large, Bacterial / Q000737:chemistry / Q000378:metabolism*; D012270:Ribosomes / Q000737:chemistry / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D016601:RNA-Binding Proteins; D011994:Recombinant Proteins; D010458:Peptidyl Transferases