A simple geometrical model of the electrostatic environment around the catalytic center of the ribosome and its significance for the elongation cycle kinetics
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.
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/Unit :
GIGA In silico medecine-Biomechanics Research Unit
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
H2020 - 772418 - INSITE - Development and use of an integrated in silico-in vitro mesofluidics system for tissue engineering
Funders :
EU - European Union F.R.S.-FNRS - Fonds de la Recherche Scientifique WELBIO - Walloon Excellence in Life Sciences and Biotechnology FWO - Fonds Wetenschappelijk Onderzoek Vlaanderen
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)
Commentary :
A '.mp4' video in supplemental material can be found online at https://doi.org/10.1016/j.csbj.2023.07.016.
Noller, H.F., Hoffarth, V., Zimniak, L., Unusual resistance of peptidyl transferase to protein extraction procedures. Science, 256, 1992, 1416.
Simonovic, M., Steitz, T., A structural view on the mechanism of the ribosome-catalyzed peptide bond formation. Biochim Biophys Acta - Gene Regul Mech, 1789, 2009, 612.
Rodnina, M., Beringer, M., Wintermeyer, W., Mechanism of peptide bond formation on the ribosome. Q Rev Biophys, 39, 2006, 203.
Rozov, A., Khusainov, I., t. El Omari, K., Importance of potassium ions for ribosome structure and function revealed by long-wavelength x-ray diffraction. Nat Commun, 10, 2019.
Nierhaus, K.H., Mg2+, K+, and the ribosome. J Bacteriol 196 (2014), 3817–3819.
Wang, J., Karki, C., Xiao, Y., Li, L., Electrostatics of prokaryotic ribosome and its biological implication. Biophys J, 118, 2020, 1205.
Rodnina, M., The ribosome in action: tuning of translational efficiency and protein folding. Protein Sci, 25, 2016.
Simpson, L.J., Tzima, E., Reader, J.S., Mechanical forces and their effect on the ribosome and protein translation machinery. Cells, 9, 2020.
Fried, S.D., Boxer, S.G., Electric fields and enzyme catalysis. Annu Rev Biochem, 86, 2017, 387.
Lu, J., Kobertz, W., Deutsch, C., Mapping the electrostatic potential within the ribosomal exit tunnel. J Mol Biol, 371, 2007, 1378.
Brooks, B., et al. CHARMM: the biomolecular simulation program. J Comput Chem, 30, 2009, 1545.
Gabdulkhakov, A., Nikonov, S., Garber, M., Revisiting the Haloarcula marismortui 50S ribosomal subunit model. Acta Crystallogr, D Biol Crystallogr, 69, 2013, 997.
Watson, Z.L., Ward, F.R., Méheust, R., Ad, O., Schepartz, A., Banfield, J.F., et al. Structure of the bacterial ribosome at 2 Å resolution. eLife, 9, 2020, e60482.
Polikanov, Y., Melnikov, S., Soll, D., Steitz, T., Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly. Nat Struct Mol Biol, 22, 2015.
Bhatt, P.R., Scaiola, A., Loughran, G., Leibundgut, M., Kratzel, A., Meurs, R., et al. Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. Science, 372, 2021, 1306.
Tirumalai, M., Rivas, M., Tran, Q., Fox, G., The peptidyl transferase center: a window to the past. Microbiol Mol Biol Rev, 85, 2021.
Doris, S., Smith, D., Beamesderfer, J., Raphael, B., Nathanson, J., Gerbi, S., Universal and domain-specific sequences in 23S–28S ribosomal RNA identified by computational phylogenetics. RNA, 21, 2015.
Sehnal, D., Svobodová Vařeková, R., Berka, K., Pravda, L., Navrátilová, V., Banáš, P., et al. MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J Cheminform, 5, 2013, 39.
Berka, K., Hanak, O., Sehnal, D., Banás, P., Navrátilová, V., Jaiswal, D., et al. MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res, 40, 2012, W222.
Pravda, L., Sehnal, D., Toušek, D., Navrátilová, V., Bazgier, V., Berka, K., et al. MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res, 46, 2018.
Beringer, M., Rodnina, M., The ribosomal peptidyl transferase. Mol Cell, 26, 2007, 311.
Lang, K., Erlacher, M., Wilson, D.N., Micura, R., Polacek, N., The role of 23S ribosomal RNA residue A 2451 in peptide bond synthesis revealed by atomic mutagenesis. Chem Biol, 15, 2008, 485.
Polikanov, Y., Steitz, T., Innis, C., A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome. Nat Struct Mol Biol, 21(9), 2014, 787.
Barton, G., Elements of Green's functions and propagation. 1989, Oxford University Press, 7–38.
Joiret, M., Kerff, F., Rapino, F., Close, P., Geris, L., Ribosome exit tunnel electrostatics. Phys Rev E, 105, 2022, 1.
Johansson, R., Numerical python. second edition, 2019, Apress, 267–293.
Lockhart, D., Kim, P., Electrostatic screening of charge and dipole interactions with the helix backbone. Science, 260, 1993, 198.
Sharp, K., Honig, B., Electrostatic interactions in macromolecules: theory and applications. Annu Rev Biophys Biophys Chem, 19, 1990, 301.
Cuervo, A., Dans, P., Carrascosa, J., Orozco, M., Gomila, G., Fumagalli, L., Direct measurement of the dielectric polarization properties of DNA. Proc Natl Acad Sci USA, 111, 2014.
van Roij R. Electrostatics in liquids: electrolytes, suspension, and emulsions, in: Lecture Notes, Institute of Theoretical Physics, Utrecht, the Netherlands, 16 July 2009, unpublished.
Sievers, A., Beringer, M., Rodnina, M., Wolfenden, R., The ribosome as an entropy trap. Proc Natl Acad Sci USA, 101, 2004, 7897.
Wallin, G., Aqvist, J., The transition state for peptide bond formation reveals the ribosome as a water trap. Proc Natl Acad Sci USA, 107, 2010, 1888.
Eyring, H., The activated complex in chemical reactions. J Chem Phys, 3, 1935, 107.
Laidler, K.J., King, M.C., Development of transition-state theory. J Phys Chem, 87, 1983, 2657.
Anslyn, E., Dougherty, D., Energy surfaces and kinetic analysis. In modern physical organic chemistry. 2005, University Science Books, Saucalito, CA, USA, 355–419.
Kaiser, C., Tinoco, I., Probing the mechanisms of translation with force. Chem Rev, 114, 2014, 3266.
Bell, G., Models for the specific adhesion of cells to cells. Science, 200, 1978, 618.
Bustamante, C., Chemla, Y.R., Forde, N.R., Izhaky, D., Mechanical processes in biochemistry. Annu Rev Biochem, 73, 2004, 705.
Ribas-Arino, J., Marx, D., Covalent mechanochemistry: theoretical concepts and computational tools with applications to molecular nanomechanics. Chem Rev, 112, 2012, 5412.
Pape, T., Wintermeyer, W., Rodnina, M., Complete kinetic mechanism of elongation factor TU-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome. EMBO J, 17, 1999, 7490.
Wohlgemuth, I., Brenner, S., Beringer, M., Rodnina, M.V., Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates. J Biol Chem, 283, 2008, 32229.
Ingolia, N., Ghaemmaghami, S., Newman, J., Weissman, J., Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324, 2009, 218.
Dana, A., Tuller, T., The effect of tRNA levels on decoding times of mRNA codons. Nucleic Acids Res, 42(14), 2014, 9171.
Dana, A., Tuller, T., Properties and determinants of codon decoding time distributions. BMC Genomics, 15, 2014, S13.
Ingolia, N.T., Lareau, L.F., Weissman, J.S., Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell, 147, 2011, 789.
Tinoco, I., Wen, J.-D., Simulation and analysis of single-ribosome translation. Phys Biol, 6, 2009, 025006.
Pavlov, M.Y., Ullman, G., Ignatova, Z., Ehrenberg, M., Estimation of peptide elongation times from ribosome profiling spectra. Nucleic Acids Res, 49, 2021, 5124.
Rodnina, M., Wintermeyer, W., Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanism. Annu Rev Biochem, 70, 2001, 415.
Fried, S., Bagchi, S., Boxer, S., Extreme electric fields power catalysis in the active site of ketosteroid isomerase. Science, 346, 2014, 1510.
Shah, P., Ding, Y., Niemczyk, M., Kudla, G., Plotkin, J., Rate-limiting steps in yeast protein translation. Cell, 153, 2013, 1589.
Nieß, A., Siemann-Herzberg, M., Takors, R., Protein production in Escherichia coli is guided by the trade-off between intracellular substrate availability and energy cost. Microb Cell Fact, 18(1), 2019, 8.
Farewell, A., Neidhardt, F.C., Effect of temperature on in vivo protein synthetic capacity in escherichia coli. J Bacteriol, 180, 1998, 4704.
Dao Duc, K., Batra, S., Bhattacharya, N., Cate, J., Song, Y., Differences in the path to exit the ribosome across the three domains of life. Nucleic Acids Res, 47, 2019.
Auffinger, P., Ennifar, E., D'Ascenso, L., Deflating the Mg2+ bubble. Stereochemistry to the rescue!. RNA, 27, 2021, 243.
Johansson, M., Ieong, K.-W., Trobro, S., Strazewski, P., Åqvist, J., Pavlov, M.Y., et al. pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the a-site aminoacyl-trna. Proc Natl Acad Sci, 108, 2011, 79.
Melnikov, S., Mailliot, J., Rigger, L., Neuner, S., Shin, B.-S., Yusupova, G., et al. Molecular insights into protein synthesis with proline residues. EMBO Rep, 17, 2016, 1776.
Pavlov, M., Watts, E., Tan, Z., Cornish, V., Ehrenberg, M., Forster, A., Slow peptide bond formation by proline and other N-alkylamino acids in translation. Proc Natl Acad Sci USA, 106, 2009, 50.
Doerfel, L., Wohlgemuth, I., Kothe, C., Peske, F., Urlaub, H., Rodnina, M., EF-P is essential for rapid synthesis of proteins containing consecutive proline residues. Science, 339, 2012.
Peil, L., Starosta, A., Lassak, J., Atkinson, G., Virumäe, K., Spitzer, M., et al. Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor ef-p. Proc Natl Acad Sci, 110, 2013.
Starosta, A.L., Lassak, J., Peil, L., Atkinson, G.C., Virumäe, K., Tenson, T., et al. Translational stalling at polyproline stretches is modulated by the sequence context upstream of the stall site. Nucleic Acids Res, 42, 2014, 10711.
Doerfel, L.K., Wohlgemuth, I., Kubyshkin, V., Starosta, A.L., Wilson, D.N., Budisa, N., et al. Entropic contribution of elongation factor p to proline positioning at the catalytic center of the ribosome. J Am Chem Soc, 137, 2015, 12997.
Levy, E., On the density for sums of independent exponential, Erlang and gamma variates. arXiv:2006.12428v4, 2020.
Ross, S., Introduction to probability models. 11th ed., 2014, Academic Press, San Diego, CA, USA, 282–361.
Erlang, A.K., Solution of some problems in the theory of probabilities of significance in automatic telephone exchanges. Brockmeyer, E., Halstrøm, H.L., Jensen, Arne, (eds.) The life and works of A.K. Erlang, Transactions of the Danish Academy of Technical Sciences, 2, Akademiet for de Tekniske Videnskaber, 1948, 138–155 archived from the original (PDF) on July 19, 2011.
Oguntunde, P., Odetunmibi, O., Adejumo, A.O., On the sum of exponentially distributed random variables: a convolution approach. Eur J Stat Probab, 2, 2014, 1.
Grushka, E., Characterization of exponentially modified Gaussian peaks in chromatography. Anal Chem, 44, 1972, 1733.
Kullback, S., Leibler, R.A., On information and sufficiency. Ann Math Stat, 22, 1951, 79.
Akaike, H., A new look at the statistical model identification. IEEE Trans Autom Control, 19, 1974, 716.
Schwarz, G., Estimating the dimension of a model. Ann Stat, 6, 1978, 461.
