Nascent peptide side chains induce rearrangements in distinct locations of the ribosomal tunnel |
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Authors: | Lu Jianli Hua Zhengmao Kobertz William R Deutsch Carol |
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Affiliation: | 1 Department of Physiology, University of Pennsylvania, PA 19104, USA2 Department of Biochemistry and Molecular Pharmacology, UMASS Medical School, Worcester, MA 01605, USA |
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Abstract: | Although we have numerous structures of ribosomes, none disclose side-chain rearrangements of the nascent peptide during chain elongation. This study reports for the first time that rearrangement of the peptide and/or tunnel occurs in distinct regions of the tunnel and is directed by the unique primary sequence of each nascent peptide. In the tunnel mid-region, the accessibility of an introduced cysteine to a series of novel hydrophilic maleimide reagents increases with increasing volume of the adjacent chain residue, a sensitivity not manifest at the constriction and exit port. This surprising result reveals molecular movements not yet resolvable from structural studies. These findings map solvent-accessible volumes along the tunnel and provide novel insights critical to our understanding of allosteric communication within the ribosomal tunnel, translational arrest, chaperone interaction, folding, and rates of elongation. |
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Keywords: | PTC, peptidyl transferase center TMA, trimethylammonium TEA, triethylammonium TPA, tripropylammonium TBA, tributylammonium PEG-MAL, polyethylene glycol maleimide MD, molecular dynamics TFA, trifluoroacetic acid ESI-MS, electrospray ionization mass spectrometry |
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