Ribosome exit tunnel electrostatics

Joiret, Marc; Rapino, Francesca; Close, Pierre; Geris, Liesbet

doi:10.1101/2020.10.20.346684

Cited by 7 publications

(16 citation statements)

References 61 publications

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“…Hence, the bare surface charge density σ * is estimated to be on the surface of the spheroid cavity around the PTC. This numerical result for the surface charge density is approximately three times higher than the surface charge density prevailing on the inner surface of the ribosome exit tunnel [15].…”

Section: Resultsmentioning

confidence: 99%

“…It was hypothesized in this study that a coarse grained permittivity should be taken in the range corresponding to a mixture of protein and water, i.e at least between = 8 and r = 78. The charges which are at a distance larger than 12 from the outer surface of the cavity are so strongly screened by the dielectric medium that they can be neglected as was detailed in [15].…”

Section: Resultsmentioning

confidence: 99%

“…The volume inside the truncated spheroid is empty, i.e., there are no 23SrRNA phosphorus atoms or ribosomal proteins charged amino acid moieties inside the volume. The charges which are at a distance larger than 12 Å from the outer surface of the cavity are so strongly screened by the dielectric medium that they can be neglected as was detailed in [15].…”

Section: Resultsmentioning

confidence: 99%

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A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome

Joiret

Rapino

et al. 2022

Preprint

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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. The electrostatic field originates from the particular 3-dimensional space distribution in the phosphate moieties of the 23S (archea and bacteria) or 28S (eukarya) rRNA of the large ribosomal subunit as well as the funnel shape of the cavity at its connection with the ribosome exit tunnel. Here, we set up a minimal geometrical model fitting the available x-ray solved structure of the ribonucleoproteic 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 expected 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) is newly incorporated in the nascent chain. Physical values of the electric field will provide quantitative knowledge of mechanical work, activation energy and kinetics of the peptide bond formation catalysed by the ribosome.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome

Joiret

Rapino

et al. 2022

Preprint

Self Cite

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“…Finally, the distribution of charged residues in the ribosome exit tunnel ( 116 ) influences the landscape of cotranslational folding. For example, the positive charge density of r-proteins in E. coli is hypothesized to play a role in the cotranslational assembly of ribosomes by delaying the release of nascent r-proteins ( 117 ).…”

Section: Discussionmentioning

confidence: 99%

Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance

Tirumalai

Anane-Bediakoh

Rajesh³

et al. 2021

Microbiol Spectr

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The net charges (at pH 7.4) of the ribosomal proteins (r-proteins) that comprise the S10-spc cluster show an inverse relationship with the halophilicity/halotolerance levels in both bacteria and archaea. In non-halophilic bacteria, the S10-spc cluster r-proteins are generally basic (positively charged), while the rest of the proteomes in these strains are generally acidic.

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“…Further studies are needed to determine whether such an effect can be observed in single-molecule experiments in vitro as well. Other attempts to build simplified folding machines to model aspects of co-translational peptide folding in vivo include the molecular-dynamics studies of folding in a tubular chamber representing the ribosome exit tunnel, either with uncharged elastic walls or with charged walls [ 183 , 184 , 185 , 186 ]. Finally, sophisticated methods of visualization and analysis of the massive dynamic data on protein folding, unfolding, and refolding are also undergoing active development (see [ 187 ] for a recent review).…”

Section: Review Of Protein Foldingmentioning

confidence: 99%

Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process?

Sorokina¹,

Mushegian

Koonin

2022

IJMS

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The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.

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Ribosome exit tunnel electrostatics

Cited by 7 publications

References 61 publications

A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome

A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome

Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance

Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process?

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