Ribosome exit tunnel electrostatics ; Belgium

peer reviewed ; The impact of ribosome exit tunnel electrostatics on the protein elongation rate or on forces acting upon the nascent polypeptide chain are currently not fully elucidated. In the past, researchers have measured the electrostatic potential inside the ribosome polypeptide exit tunnel at a limited number of spatial points, at least in rabbit reticulocytes. Here we present a basic electrostatic model of the exit tunnel of the ribosome, providing a quantitative physical description of the tunnel interaction with the nascent proteins at all centro-axial points inside the tunnel. We s... Mehr ...

Verfasser: Joiret, Marc
Kerff, Frédéric
Rapino, Francesca
Close, Pierre
Geris, Liesbet
Dokumenttyp: journal article
Erscheinungsdatum: 2022
Verlag/Hrsg.: American Physical Society
Schlagwörter: Ribosome / Biophysics / x-ray crystallography / electrostatic interaction / force sensing / TASEP / co-translational protein folding / RNA-protein interaction / optical tweezers / Life sciences / Biochemistry / biophysics & molecular biology / Sciences du vivant / Biochimie / biophysique & biologie moléculaire
Sprache: Englisch
Permalink: https://search.fid-benelux.de/Record/base-26593098
Datenquelle: BASE; Originalkatalog
Powered By: BASE
Link(s) : https://orbi.uliege.be/handle/2268/267021

peer reviewed ; The impact of ribosome exit tunnel electrostatics on the protein elongation rate or on forces acting upon the nascent polypeptide chain are currently not fully elucidated. In the past, researchers have measured the electrostatic potential inside the ribosome polypeptide exit tunnel at a limited number of spatial points, at least in rabbit reticulocytes. Here we present a basic electrostatic model of the exit tunnel of the ribosome, providing a quantitative physical description of the tunnel interaction with the nascent proteins at all centro-axial points inside the tunnel. We show that a strong electrostatic screening is due to water molecules (not mobile ions) attracted to the ribosomal nucleic acid phosphate moieties buried in the immediate vicinity of the tunnel wall. We also show how the tunnel wall components and local ribosomal protein protrusions impact on the electrostatic potential profile and impede charged amino acid residues from progressing through the tunnel, affecting the elongation rate in a range of −40% to +85% when compared to the average elongation rate. The time spent by the ribosome to decode the genetic encrypted message is constrained accordingly. We quantitatively derive, at single-residue resolution, the axial forces acting on the nascent peptide from its particular sequence embedded in the tunnel. The model sheds light on how the experimental data point measurements of the potential are linked to the local structural chemistry of the inner wall, shape, and size of the tunnel. The model consistently connects experimental observations coming from different fields in molecular biology, x-ray crystallography, physical chemistry, biomechanics, and synthetic and multiomics biology. Our model should be a valuable tool to gain insight into protein synthesis dynamics, translational control, and the role of the ribosome's mechanochemistry in the cotranslational protein folding. ; FNRS-FWO EOS Grant No. 30480119 (Join-t-against-Osteoarthritis); WELBIO CR2017S02 (THERAtRAME);ERC ...