Article (Scientific journals)
A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome and its significance for the elongation cycle kinetics
Joiret, Marc; Kerff, Frédéric; Rapino, Francesca et al.
2023In Computational and Structural Biotechnology Journal, 21, p. 3768-3795
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Convolution.mp4
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video caption: Ribosome residence time (RRT) distribution on a codon. The time spent by the ribosome on a codon is stochastic. It results from the queuing time theory in probability and statistics. The RRT distribution can be modelled as the convolution product of three exponentially distributed time distributions, each of which representing the three sequential sub-steps of the elongation cycle. This convolution product is the hypo-exponential distribution. The video shows how the convolution product is calculated and the quality of the fit to similarly skewed distributions like the gamma distribution and the exponentially modified Gaussian distribution.
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Keywords :
Computer Science Applications; Genetics; Biochemistry; Structural Biology; Biophysics; Biotechnology; Computational biology; X-ray crystallography; queueing time theory; protein elongation; ribosome; tRNA; mRNA translation; peptide bond formation; peptidyl transferase center
Abstract :
[en] The central function of the large subunit of the ribosome is to catalyze peptide bond formation. This biochemical reaction is conducted at the peptidyl transferase center (PTC). Experimental evidence shows that the catalytic activity is affected by the electrostatic environment around the peptidyl transferase center. Here, we set up a minimal geometrical model fitting the available x-ray solved structures of the ribonucleic cavity around the catalytic center of the large subunit of the ribosome. The purpose of this phenomenological model is to estimate quantitatively the electrostatic potential and electric field that are experienced during the peptidyl transfer reaction. At least two reasons motivate the need for developing this quantification. First, we inquire whether the electric field in this particular catalytic environment, made only of nucleic acids, is of the same order of magnitude as the one prevailing in catalytic centers of the proteic enzymes counterparts. Second, the protein synthesis rate is dependent on the nature of the amino acid sequentially incorporated in the nascent chain. The activation energy of the catalytic reaction and its detailed kinetics are shown to be dependent on the mechanical work exerted on the amino acids by the electric field, especially when one of the four charged amino acid residues (R, K, E, D) has previously been incorporated at the carboxy-terminal end of the peptidyl-tRNA. Physical values of the electric field provide quantitative knowledge of mechanical work, activation energy and rate of the peptide bond formation catalyzed by the ribosome. We show that our theoretical calculations are consistent with two independent sets of previously published experimental results. Experimental results for E.coli in the minimal case of the dipeptide bond formation when puromycin is used as the final amino acid acceptor strongly support our theoretically derived reaction time courses. Experimental Ribo-Seq results on E. coli and S. cerevisiae comparing the residence time distribution of ribosomes upon specific codons are also well accounted for by our theoretical calculations. The statistical queueing time theory was used to model the ribosome residence time per codon during nascent protein elongation and applied for the interpretation of the Ribo-Seq data. The hypo-exponential distribution fits the residence time observed distribution of the ribosome on a codon. An educated deconvolution of this distribution is used to estimate the rates of each elongation step in a codon specific manner. Our interpretation of all these results sheds light on the functional role of the electrostatic profile around the PTC and its impact on the ribosome elongation cycle.
Research center :
GIGA In silico medecine-Biomechanics Research Unit
Disciplines :
Biochemistry, biophysics & molecular biology
Physics
Physical, chemical, mathematical & earth Sciences: Multidisciplinary, general & others
Chemistry
Author, co-author :
Joiret, Marc  ;  Université de Liège - ULiège > GIGA
Kerff, Frédéric  ;  Université de Liège - ULiège > Département des sciences de la vie > Centre d'Ingénierie des Protéines (CIP)
Rapino, Francesca  ;  Université de Liège - ULiège > Département de pharmacie
Close, Pierre  ;  Université de Liège - ULiège > Département de pharmacie
Geris, Liesbet  ;  Université de Liège - ULiège > Département d'aérospatiale et mécanique > Génie biomécanique
Language :
English
Title :
A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome and its significance for the elongation cycle kinetics
Publication date :
July 2023
Journal title :
Computational and Structural Biotechnology Journal
eISSN :
2001-0370
Publisher :
Elsevier BV
Volume :
21
Pages :
3768-3795
Peer reviewed :
Peer Reviewed verified by ORBi
European Projects :
H2020 - 772418 - INSITE - Development and use of an integrated in silico-in vitro mesofluidics system for tissue engineering
Funders :
EU - European Union [BE]
F.R.S.-FNRS - Fonds de la Recherche Scientifique [BE]
WELBIO - Walloon Excellence in Life Sciences and Biotechnology [BE]
FWO - Fonds Wetenschappelijk Onderzoek Vlaanderen [BE]
Funding number :
H2020/2014-2020/ERC grant agreement n°772418 (INSITE); FNRS-FWO EOS grant n°30480119 (Joint-t-against-ostheoarthritis); FNRS-WELBIO grant n°WELBIO-CR-2017S-02 (THERA-tRAME)
Data Set :
https://doi.org/10.1016/j.csbj.2023.07.016

A '.mp4' video in supplemental material can be found online at https://doi.org/10.1016/j.csbj.2023.07.016.

Commentary :
A '.mp4' video in supplemental material can be found online at https://doi.org/10.1016/j.csbj.2023.07.016.
Available on ORBi :
since 01 September 2023

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