Seminar

Structural studies on nascent chain ribosomal complexes. Getting ready for THE SECOND CODE

Paola Fucini, PhD

Emerging biochemical and biophysical data strongly suggest that the transformation of the potential set of proteins, encrypted in the genome of the cell, into its actual vital functional set, is a function not just of the genetic code but of an additional layer of information encoded within the newly synthesized polypeptide nascent chain (NC). To date, we know that immediately upon the first steps of protein synthesis, a variety of signals are formed within the evolving nascent chain (NC). These signals, by acting directly on the ribosome or by recruiting additional cellular machines, have the ability to dictate and direct new steps in the transformation of the NC, guiding it towards the acquisition of its final functional state and cellular location. Due to its distinct nature, I prefer to refer to this ensemble of signals as THE SECOND CODE. Despite our knowledge of its existence and importance, today we know very little about its mechanism of action. The aim of my talk is to give an overview on the latest unpublished results from our group that entail: 1) the competition/cooperation between SecA and TF on the ribosome (using the Methyl-Trosy approach, by solution state NMR) 2) the mode of binding of SecA on stalled nascent chain ribosomal complexes (using CryoEM, in collaboration with Prof. Kuhlbrandt - Max Plank Institute for Biophysics and Dr. Sean Connell - Frankfurt University, Frankfurt am Main) 3) the visualization by X-ray crystallography of a cascade of events, started by a NC mimic in the ribosomal tunnel and ending at the peptidyl transferase center, altering its configuration, to impare peptide bond formation. The results obtained have thus settled a solid research line and experimental approach to unravel the molecular determinants of the second code and to decipher how the signals, embedded in the NC, orchestrate the concerted action of the ribosome and its ancillary factors (i,e, SecA, SecB, TF and the translocon) to drive its own transformation into a functional protein.