Department of Cell and Molecular Biology

Publications

2017

Zhang J, Pavlov MY and Ehrenberg M.  Accuracy of genetic code translation and its orthogonal corruption by  aminoglycosides and Mg2+ ions Nucleic Acids Research. 2017.  In press

Caban K, Pavlov M, Ehrenberg M, Gonzalez RL Jr. A conformational switch in initiation factor 2 controls the fidelity of translation initiation in bacteria. Nat Commun. 2017 Nov 14;8(1):1475. doi: 10.1038/s41467-017-01492-6

Mellenius H, Ehrenberg M. Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase. Nucleic Acids Res. 2017 Sep 28. doi: 10.1093/nar/gkx849. [Epub ahead of print] PMID: 29036494 Similar articles: Select item 28726822

Reuveni S, Ehrenberg M, Paulsson J. Ribosomes are optimized for autocatalytic production. Nature. 2017 Jul 19;547(7663):293-297. doi: 10.1038/nature22998. PMID: 28726822 Similar articles: Select item 28138071

Pavlov MY, Liljas A, Ehrenberg M. A recent intermezzo at the Ribosome Club. Philos Trans R Soc Lond B Biol Sci. 2017 Mar 19;372(1716). pii: 20160185. doi: 10.1098/rstb.2016.0185. Review. PMID: 28138071 Free PMC Article

Harish A, Kurland CG. Mitochondria are not captive bacteria. J Theor Biol.2017 Dec 7;434:88-98. doi: 10.1016/j.jtbi.2017.07.011. Epub 2017 Jul 25. PubMed PMID: 28754286.

Harish A, Kurland CG. Empirical genome evolution models root the tree of life. Biochimie. 2017 Jul;138:137-155. doi: 10.1016/j.biochi.2017.04.014. Epub 2017 May 4. PubMed PMID: 28478110.

Harish A, Kurland CG. Akaryotes and Eukaryotes are independent descendants of a universal common ancestor. Biochimie. 2017 Jul;138:168-183. doi:10.1016/j.biochi.2017.04.013. Epub 2017 Apr 28. PubMed PMID: 28461155.

2016

Harish A, Abroi A, Gough J, Kurland C. Did Viruses Evolve As a Distinct Supergroup from Common Ancestors of Cells? Genome Biol Evol. 2016 Aug 27;8(8):2474-81. doi: 10.1093/gbe/evw175. PubMed PMID: 27497315; PubMed Central PMCID: PMC5010908.

Ieong KW, Uzun Ü, Selmer M, Ehrenberg M. (2016) Two proofreading steps amplify the accuracy of genetic code translation. Proc Natl Acad Sci U S A. 113(48):13744-13749 link

Fu Z, Kaledhonkar S, Borg A, Sun M, Chen B, Grassucci RA, Ehrenberg M, Frank J. (2016) Key Intermediates in Ribosome Recycling Visualized by Time-Resolved Cryoelectron Microscopy. Structure. 24(12):2092-2101 link

Zhang J, Ieong KW, Mellenius H, Ehrenberg M. (2016) Proofreading neutralizes potential error hotspots in genetic code translation by transfer RNAs.RNA. 22(6):896-904 link

Borg A, Pavlov M, Ehrenberg M. (2016) Mechanism of fusidic acid inhibition of RRF- and EF-G-dependent splitting of the bacterial post-termination ribosome. Nucleic Acids Res. 44(7):3264-75 link

Holm M., Borg A., Ehrenberg M. and Sanyal S. (2016) Molecular mechanism of viomycin inhibition of peptide elongation in bacteria. Proc Natl Acad Sci U S A 113(4):978-83 link

Choi J, Ieong KW, Demirci H, Chen J, Petrov A, Prabhakar A, O’Leary SE, Dominissini D, Rechavi G, Soltis SM, Ehrenberg M, Puglisi JD. (2016) N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics. Nat Struct Mol Biol. 23(2):110-5 link

Borg A., Pavlov M. and Ehrenberg M. (2016) Complete kinetic mechanism for recycling of the bacterial ribosome. RNA 22(1):10-21 link

2015

Kurland CG, Harish A. Structural biology and genome evolution: An introduction. Biochimie. 2015 Dec;119:205-8. doi: 10.1016/j.biochi.2015.10.023. Epub 2015 Nov 4. PubMed PMID: 26546841.

Kurland CG, Harish A. The phylogenomics of protein structures: The backstory. Biochimie. 2015 Dec;119:284-302. doi: 10.1016/j.biochi.2015.07.027. Epub 2015 Jul 31. Review. PubMed PMID: 26234735.

Patrick M., Dennis P.P., Ehrenberg M. and Bremer H. (2015) Free RNA polymerase in Escherichia coli. Biochimie 119:80-91 link

Zhang J., Ieong K.W., Johansson M. and Ehrenberg M. (2015) Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome. Proc Natl Acad Sci U S A 112(31):9602-7 link

Borg A. and Ehrenberg M. (2015) Determinants of the rate of mRNA translocation in bacterial protein synthesis. J Mol Biol 427(9):1835-47 link

Mellenius H. and Ehrenberg M. (2015) DNA template dependent accuracy variation of nucleotide selection in transcription. PLoS One 10(3):e0119588 link

Indrisiunaite G., Pavlov M.Y., Heurgué-Hamard V. and Ehrenberg M. (2015) On the pH Dependence of Class-1 RF-Dependent Termination of mRNA Translation. J Mol Biol pii:S0022-2836(15)00028-5 link

Borg A., Holm M., Shiroyama I., Hauryliuk V., Pavlov M., Sanyal S. and Ehrenberg M. (2015) Fusidic acid targets elongation factor G in several stages of translocation on the bacterial ribosome. J Biol Chem 290(6):3440-54 link

2014

Borg A. and Ehrenberg M. (2014) Determinants of the rate of mRNA translocation in bacterial protein synthesis. J Mol Biol pii:S0022-2836(14)00583-X link

Wang J., Kwiatkowski M., Pavlov M.Y., Ehrenberg M. and Forster A.C. (2014) Peptide formation by N-methyl amino acids in translation is hastened by higher pH and tRNA(Pro). ACS Chem Biol 9(6):1303-11 link

Ieong K.W., Pavlov M.Y., Kwiatkowski M., Ehrenberg M. and Forster A.C. (2014) A tRNA body with high affinity for EF-Tu hastens ribosomal incorporation of unnatural amino acids. RNA 20(5):632-43 link

Fange D., Mellenius H., Dennis P.P. and Ehrenberg M. (2014) Thermodynamic modeling of variations in the rate of RNA chain elongation of E. coli rrn operons. Biophys J 106(1):55-64 link

2013

Pavlov M.Y. and Ehrenberg M. (2013) Optimal control of gene expression for fast proteome adaptation to environmental change. Proc Natl Acad Sci USA 110(51):20527-32 link

Pallesen J., Hashem Y., Korkmaz G., Koripella R.K., Huang C., Ehrenberg M., Sanyal S. and Frank J. (2013) Cryo-EM visualization of the ribosome in termination complex with apo-RF3 and RF1. Elife 2:e00411 link

Tsai A., Uemura S., Johansson M., Puglisi E.V., Marshall R.A., Aitken C.E., Korlach J., Ehrenberg M. and Puglisi J.D. (2013) The impact of aminoglycosides on the dynamics of translation elongation. Cell Rep 3(2):497-508 link

Ehrenberg M., Bremer H. and Dennis P.P. (2013) Medium-dependent control of the bacterial growth rate. Biochimie 95(4):643-58. Review link

Liljas, A. and Ehrenberg, M. Series in Structural Biology-Vol 1. (2013). Structural Aspects of Protein Synthesis. 2nd Edition. 420 pages. World Scientific Publishing Co. Pte. Ltd.

Mellenius H. and Ehrenberg M. (2013) Large DNA template dependent error variation during transcription. Biophysics and Structure to Counter Threats and Challenges. NATO Science for Peace and Security Series. Edited by: J.D. Puglisi, 3:39-57 link

2012

Ieong K.W., Pavlov M.Y., Kwiatkowski M., Forster A.C. and Ehrenberg M. (2012) Inefficient delivery but fast peptide bond formation of unnatural L-aminoacyl-tRNAs in translation. J Am Chem Soc 134(43):17955-62 link

Johansson M., Zhang J., Ehrenberg M. (2012) Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection. PNAS 109:131 link

Shyp V., Tankov S., Ermakov A., Kudrin P., English B.P., Ehrenberg M., Tenson T., Elf J. and Hauryliuk V. (2012) Positive allosteric feedback regulation of the stringent response enzyme RelA by its product. EMBO Reports 13(9):835-9 link

2011

Liljas A, Ehrenberg M, Åqvist J. (2011) Comment on "The mechanism for activation of GTP hydrolysis on the ribosome". Science 333:37 link

Fange D, Lovmar M, Pavlov MY, Ehrenberg M. (2011) Identification of enzyme inhibitory mechanisms from steady-state kinetics. Biochimie 93:1623-9 link

Johansson M., Ieong K. W., Trobro S., Strazewski P., Åqvist J., Pavlov M. Y., and Ehrenberg M. (2011) pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA. PNAS 108:79-84 link

Pavlov M. Y., Zorzet A., Andersson D. I., Ehrenberg M. (2011) Activation of initiation factor 2 by ligands and mutations for rapid docking of ribosomal subunits. EMBO J 30:289-301 link

Pavlov M., Sanyal S., Ehrenberg M. (2011) Initiation of bacterial protein synthesis with wild type and novel mutants of initiation factor 2 in Ribosomes: Structure, Function and Dynamics. eds. Rodnina M., Wintermeyer W., Green R., Springer Verlag GmbH link

Johansson M., Ieong K. W., Åqvist, J., Pavlov M. Y., Ehrenberg M. (2011) Rate and accuracy of ribosomal peptidyl transfer in Ribosomes: Structure, Function and Dynamics. eds. Rodnina M., Wintermeyer W., Green R., Springer Verlag GmbH link

2010

Mitkevich VA, Ermakov A, Kulikova AA, Tankov S, Shyp V, Soosaar A, Tenson T, Makarov AA, Ehrenberg M, Hauryliuk V. (2010) Thermodynamic characterization of ppGpp binding to EF-G or IF2 and of initiator tRNA binding to free IF2 in the presence of GDP, GTP, or ppGpp J Mol Biol 402:838-46. link

Ehrenberg M. (2010) Protein synthesis: Translocation in slow motion Nature 466:325-6. link

Tobin C., Mandava C.S., Ehrenberg M., Andersson D.I., Sanyal, S. (2010) Ribosomes lacking protein S20 are defective in mRNA binding and subunit association J Mol Biol 397:767-76. link

Zorzet A., Pavlov M., Nilsson A., Ehrenberg M., Andersson D. (2010) Error-prone initiation factor 2 mutants reduce the fitness cost of antibiotic resistance. Mol Microbiol 75:1299-1313. link

2009

Ivanova N., Scheres S. H., Pavlov M. Y., Carazo J. M.; Hebert H., Ehrenberg M., Lindahl M., Cheng K. (2010) tmRNA·SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes. J Struct Biol 169:342-348 link

Hauryliuk V., Mitkevich V. A., Draycheva A., Tankov S., Shyp V., Ermakov A., Kulikova A. A. , Makarov A. A., Ehrenberg M. (2009) Thermodynamics of GTP and GDP binding to bacterial initiation factor 2 suggests two types of structural transitions. J Mol Biol 394:621-6 link

Ehrenberg M., Dennis P. P., Bremer H. (2010) Maximum rrn promoter activity in Escherichia coli at saturating concentrations of free RNA polymerase. Biochimie 92:12-20. link

Lovmar M, Vimberg V, Lukk E, Nilsson K, Tenson T, Ehrenberg M. (2009) Cis-acting resistance peptides reveal dual ribosome inhibitory action of the macrolide josamycin. Biochimie 91:989-95 link

Fange D, Nilsson K, Tenson T, Ehrenberg M. (2009) Drug efflux pump deficiency and drug target resistance masking in growing bacteria. Proc Natl Acad Sci USA 106:8215-20 link

Dennis P, Ehrenberg M, Fange D, Bremer H. (2009) Varying rate of RNA chain elongation during rrn transcription in E. coli. J Bacteriol 191:3740-6 link

Lovmar M, Nilsson K, Lukk E, Vimberg V, Tenson T and Ehrenberg M (2009) Erythromycin resistance by L4/L22 mutations and resistance masking by drug efflux pump deficiency. EMBO J 28:736-44 link

Sengupta J, Villa E, Trabuco LG, LeBarron J, Baxter WT, Shaikh TR, Grassucci RA, Nissen P, Ehrenberg M, Schulten K, Frank J. (2009) Ribosome-induced Changes in EF-Tu Conformation: The Mechanism of GTP Hydrolysis. Proc Natl Acad Sci USA 106:1063-8 link

Pavlov MY, Watts RE, Tan Z, Cornish VW, Ehrenberg M, Forster AC. (2009) Slow peptide formation by proline and other N-alkyl amino acids in translation. Proc Natl Acad Sci USA 106:50-4 link

Ehrenberg, M. Scientific Background on the Nobel Prize in Chemistry 2009. Structure and Function of the Ribosome.

2008

Li W, Agirrezabala X, Lei J, Bouakaz L, Brunelle JL, Ortiz-Meoz RF, Green R, Sanyal S, Ehrenberg M, and Frank J. (2008) Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM. EMBO J 27:3322-31 link

Hauryliuk V, Mitkevich VA, Eliseeva NA, Petrushanko I Yu, Ehrenberg M, Makarov AA. (2008) The pretranslocation ribosome is targeted by GTP-bound EF-G in partially activated form. Proc Natl Acad Sci USA 105:15678-83 link

Michel BY, Krishnakumar KS, Johansson M, Ehrenberg M, Strazewski P (2008) Structural and functional prerequisites for ribosomal nascent peptide acceptors: attempts to decipher the nature of the ribosome's catalysis of peptide bond formation. Nucleic Acids Symp Ser (Oxf) 52:33-34 link

Pavlov M, Antoun A, Lovmar M and Ehrenberg M (2008) Complementary roles of initiation factor 1 and ribosome recycling factor in 70S ribosome splitting. EMBO J 27:1706-17 link

Hauryliuk V, Hansson S, Ehrenberg M. (2008) Co-factor dependent conformational switching of GTPases. Biophys J 95:1704-15 link

Johansson M, Bouakaz E, Lovmar M, Ehrenberg M. (2008) The kinetics of ribosomal peptidyl-transfer revisited. Mol Cell 30:589-598 link

Nilsson K, and Ehrenberg M. (2008) A novel mechanism for activation controlled initiation of DNA replication that resolves the auto-regulation sequestration paradox in Lecture Notes Physics: Aspects of Physical Biology: Biological Water, Protein Solutions, Transport and Replication.

Johansson M, Lovmar M, Ehrenberg M. (2008) Rate and accuracy of bacterial protein synthesis revisited. Curr Opin Microbiol 11:141-7 link

Andreev D, Hauryliuk V, Terenin I, Dmitriev S, Ehrenberg M, Shatsky I. (2008) The bacterial toxin RelE induces specific mRNA cleavage in the A site of the eukaryote ribosome. RNA 14:233-9. link

Ehrenberg, M. Scientific Background on the Nobel Prize in Chemistry 2008. The green fluorescent protein: discovery, expression and development. link

2007

Gao N, Zavialov AV, Ehrenberg M, Frank J. (2007) Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits. J Mol Biol 374:1345-58. link

Gao H., Zhou Z., Rawat U., Huang C., Bouakaz L., Wang C., Cheng Z., Liu Y., Zavialov A., Gursky R., Sanyal S., Ehrenberg M., Frank J., Song H. (2007). RF3 induces ribosomal conformational changes responsible for the dissociation of class-I release factors. Cell 129:929-41. link

Ivanova, N., Lindell, M., Pavlov, M., Holmberg-Schiavone, L., Wagner E.G.H. and Ehrenberg, M. (2007). Structure probing of tmRNA in distinct stages of trans-translation. RNA 13:713-22 link

2006

Ehrenberg, M., Hauryliuk, V., Crist, C.C. and Nakamura, Y. (2006). Translation Termination, the Prion [Psi+], and Ribosomal Recycling. In Translational control in biology and medicine. Michael B. Mathews, Nahum Sonenberg, John W.B. Hershey.

Elf J, Nilsson K, Tenson T, Ehrenberg M. (2006).Bistable Bacterial Growth Rate in Response to Antibiotics with Low Membrane Permeability. Phys Rev Lett 97:258104. link

Raine A, Lovmar M, Wikberg J, Ehrenberg M. (2006). Trigger factor binding to ribosomes with nascent peptide chains of varying lengths and sequences. J Biol Chem 281:28033-8. link

Hauryliuk V, Zavialov A, Kisselev L, Ehrenberg M. (2006). Class-1 release factor eRF1 promotes GTP binding by class-2 release factor eRF3. Biochimie 88:747-57. link

Antoun A., Pavlov M.Y., Lovmar M. and Ehrenberg M. (2006). How initiation factors tune the rate of initiation of protein synthesis in bacteria. EMBO J 23:183-93 link

Lovmar, M. and Ehrenberg, M. (2006). Rate, accuracy and cost of ribosomes in bacterial cells. Biochimie 88:951-61 link

Antoun A., Pavlov M.Y., Lovmar M. and Ehrenberg M. (2006). How initiation factors maximize accuracy of initiation of bacterial protein synthesis. Mol Cell 25:2539-50 link

David Fange and Johan Elf (2006) Noise induced Min phenotypes in E. coli. PLoS Comp Biol 2:e80

Hauryliuk V and Ehrenberg M. (2006). Two-step selection of mRNAs in initiation of protein synthesis. Mol Cell 22:155-6 link

Frank, J., Rawat, U., Gao, H., Zavialov A., Gursky, R., Ehrenberg, M. (2006) Interactions of the Release Factor RF1 with the Ribosome as Revealed by Cryo-EM. J Mol Biol 357:1144-53 link

Lovmar, M., Nilsson, K., Vimberg, V., Tenson, T., Nervall, M., and Ehrenberg M. (2006) The molecular mechanism of peptide mediated erythromycin resistance J Biol Chem 281:6742-50. link

2005

Vestergaard, B., Sanyal, S., Roessle, M., Mora, L., Buckingham, RH, Kastrup, JS, Gajhede, M., Svergun, DI and Ehrenberg, M. (2005) The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure. Mol Cell 20:929-938

Bouakaz, L., Bouakaz, E., Murgola, EJ, Ehrenberg, M. and Sanyal, S. (2005) The role of ribosomal protein L11 in class-I release factor mediated translation termination and translational accuracy. J Biol Chem 281:4548-56.

Sörensen, M., Elf, J., Bouakaz, E., Tenson, T., Sanyal, S., Björk, GR and Ehrenberg, M. (2005) Selective charging of leucine tRNAs reveals new codon reading and tRNA modification. J Mol Biol 354:16-24

Gao, N., Zavialov, AV, Li, W., Sengupta, J., Valle, M. Gursky, RP, Ehrenberg, M and Frank, J. (2005) Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. Mol Cell 18:663-674

Ivanova, N., Pavlov, MY, Bouakaz, E., Ehrenberg, M. and Holmberg Schiavone, L. (2005) Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA. Nucleic Acids Res 33:3529-3539

Zavialov, AV, Hauryliuk, V and Ehrenberg, M. (2005) Splitting of the post-termination ribosome into subunits by the concerted action of RRF and EF-G. Molecular Cell 18:663-674

Ivanova, N., Pavlov, M. and Ehrenberg, M. (2005) tmRNA induced release of messenger RNA from stalled ribosomes. J Mol Biol 29:897-905

Allen, GS, Zavialov, AV, Gursky, R., Ehrenberg, M. and Frank, J. (2005) The Solution Structure of a Translation Initiation Complex from Escherichia coli at 13.8 Å. Cell 12:703-712

Elf J. and Ehrenberg, M. (2005) What makes ribosome dependent transcriptional attenuation sensitive to amino acid limitation? 1:e2 PLoS Computational Biology

Frank J., Sengupta, J. Gao, H., Li W, Valle, M. Zavialov, A. and Ehrenberg, M. (2005) The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl- transfer. FEBS Lett 579 959-962.

Hennely, SP, Antoun, A., Ehrenberg, M., Gualerzi, CO, Knight, W, Lodmell, JS, and Hill, WE.(2005) A time-resolved investigation of ribosomal subunit association. J Mol Biol 366 1243-1258.

Paulsson, J and Elf, J (2005) Stochastic Modeling of Intracellular Kinetics. Book chapter in System Modeling in Cellular Biology eds. Zoltan Szallasi, Vipul Periwal & Jörg Stelling, MIT press.

Elf, J, Paulsson, J, Berg, O and Ehrenberg, M, Mesoscopic kinetics and its applications in protein synthesis, (2005) Ed. Stefan Hohman, book chapter, Springer Verlag

Zavialov, AV, Hauryliuk, V and Ehrenberg, M. (2005) Guanine nucleotide exchange on ribosome bound elongation factor G initiates translocation of tRNAs. Journal of Biology 4(2):9

Hattne J, Fange D, and Elf J (2005) Stochastic reaction-diffusion simulation with MesoRD Bioinformatics.

Lindsley D, Bonthuis P, Gallant J, Tofoleanu T, Elf J and Ehrenberg M (2005) Ribosome By-passing At Serine Codons as a Test of the Model of Selective tRNA. Charging EMBO reports 6 147-150 download pdf

Dittmar K, Sørensen M, Elf J, Ehrenberg M, Pan T, (2005) Microarrays reveal selective charging of tRNA isoacceptors during amino acid starvation. EMBO reports 6 151-157 download pdf

Elf, J and Ehrenberg, M (2005) Near-critical behavior of aminoacyl-tRNA pools in E. coli at rate limiting supply of amino acids. Biophysical J 88 132-46 download pdf

2004

Lovmar, M, Tenson, T, Ehrenberg, M (2004) Kinetics of macrolide action: The josamycin and erythromycin cases. J Biol Chem 279 53506-15 download pdf

Elf, J and Ehrenberg, M (2004) Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases. Systems Biology 2 download pdf Supplementary Material

Dennis, P, Ehrenberg, M and Bremer H (2004) Control of ribosomal RNA synthesis in Escherichia coli:a systems biology approach. Microbiol Mol Biol Rev 68 639-68 download pdf

Gao, H, Valle, M, Ehrenberg, M and Frank, J. (2004) Dynamics of EF-G interaction with the ribosome explored by classification of hetrogeneous cryo-EM dataset. J Struct. Biol 147 283-290. download pdf

Raine A, Ivanova N, Wikberg JE, Ehrenberg M. (2004) Simultaneous binding of trigger factor and signal recognition particle to the E. coli ribosome. Biochimie 86 495-500.

Antoun A, Pavlov MY, Tenson T, Ehrenberg M Ma. (2004) Ribosome formation from subunits studied by stopped-flow and Rayleigh light scattering. Biol Proced Online 6 35-54.

Hallier M, Ivanova N, Rametti A, Pavlov M, Ehrenberg M, Felden B. (2004) Pre-binding of small protein B to a stalled ribosome triggers trans-translation. J Biol Chem 279 25978-85.

Ivanova N, Pavlov MY, Felden B, Ehrenberg M. (2004) Ribosome rescue by tmRNA requires truncated mRNAs. J Mol Biol 16 33-41.

Software: Hattne J and Elf J. (2004) MesoRD

2003

Mikel Valle, Andrey Zavialov, Wen Li, Scott M Stagg, Jayati Sengupta, Rikke C Nielsen, Poul Nissen, Stephen C Harvey, Måns Ehrenberg & Joachim Frank (2003) Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy Nat. Struct. Biol.

Mora L, Zavialov A, Ehrenberg M, Buckingham RH. (2003) Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli. Mol Microbiol 50 1467-1476.

Antoun A, Pavlov MY, Andersson K, Tenson T, Ehrenberg M. (2003) The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis. EMBO J, 22 5593-5601

Bremer H, Dennis P, Ehrenberg M. (2003) Free RNA polymerase and modeling global transcription in Escherichia coli. Biochimie, 85 597-609

Ehrenberg M, Elf J, Aurell E, Sandberg R and Tegnér, J (2003) Systems Biology is Taking Off. Genome Research 13 2377-2380

Elf, J and Ehrenberg, M (2003) Fast evaluation of fluctuations in biochemical networks with the linear noise approximation. Genome Research 13 2475-2484

Raine A, Ullers R, Pavlov M, Luirink J, Wikberg J and Ehrenberg M. (2003) Targeting and insertion of heterologous membrane proteins in E.coli. Biochimie, 85 659-668

Tenson T, Lovmar M, Ehrenberg M. (2003) The mechanism of action of macrolides, lincosamides and streptogramin B reveals the nascent Peptide exit path in the ribosome. J Mol Biol 330 1005-14.

Zavialov, AV and Ehrenberg, M. (2003) Peptidyl-tRNA regulates the GTPase activity of translation factors Cell 114 113-122

Valle M, Zavialov A, Sengupta J, Rawat U, Ehrenberg M, Frank J. (2003) Locking and unlocking of ribosomal motions. Cell 114 123-134

Elf, J, Nilsson, D, Tenson, T and Ehrenberg, M. (2003) Selective charging of tRNA isoacceptors explains petterns of codon usage Science 300, 1718-1722

Pedersen, K., Zavialov, A., Pavlov, M., Elf, J., Gerdes, K. and Ehrenberg, M. (2003) The bacterial toxin RelE displays codon specific cleavage of mRNAs in the ribosomal A-site. Cell 112, 131-140

Klaholz, B.P., Pape, T.,. Zavialov, A.V., Myasnikov, A.G., Orlova, E.V., Vestergaard, B., Ehrenberg, M. and van Heel, M. (2003) Structure of the E. coli ribosomal termination complex with release factor 2. Nature 421, 90-94

Rawat, U.B.S., Zavialov, A.V., Sengupta, J., Valle, M., Grassucci, R.A., Linde, J., Vestergaard, B., Ehrenberg, M. and Frank, J (2003) A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature 421, 87-90

Ullers RS, Houben EN, Raine A, Ten Hagen-Jongman CM, Ehrenberg M, Brunner J, Oudega B, Harms N, Luirink J. (2003) Interplay of signal recognition particle and trigger factor at L23 near the nascent chain exit site on the Escherichia coli ribosome. J Cell Biol 161, 679-684

Mora, L., Heurgué-Hamard, V., Champ, S., Ehrenberg, M., Kisselev, L.L. and Buckingham, R.H. (2003) The essential role of the invariant GGQ motif in the function and the stability in vivo of bacterial release factors RF1 and RF2. Molecular Microbiology 47, 267-275

Elf J., Paulsson J., Berg O. & Ehrenberg M. (2003) Near-critical phenomena in intracellular metabolite pools. Biophysical J 84, 154-170

Kisselev, L., Ehrenberg, M., and Frolova, L. (2003) Termination of translation: interplay of mRNA, rRNAs and release factors? EMBO J 22, 175-182

2002

Zhang, X., Dennis, P., Ehrenberg, M. and H. Bremer, H. (2002). Kinetic properties of rrn promoters in Escherichia coli. Biochimie 84 981-96

Zavialov, A.V., Mora, L., Buckingham, R.H., and Ehrenberg, M. (2002). Release of Peptide Promoted by the GGQ-Motif of Class 1 Release Factors Regulates the GTPase Activity of RF3. Molecular Cell 10, 789-798.

Ortega, F., Ehrenberg, M., Acerenza, L., Westerhoff, H.V. and Cascante, M. (2002). Sensitivity analysis of metabolic cascades catalyzed by bifunctional enzymes.Mol. Biol. Rep.29, 211-215.

Zhenyu Gu, Marianne Weidenhaupt, Natalia Ivanova, Michail Pavlov, Bingze Xu, Zhi-Guo Su and Jan-Christer Janson (2002) Chromatographic Methods for the Insolation of, and Refolding of Proteins from, Escherichia coli Inclusion Bodies. Protein expression and purification 25, 174-179.

Ehrenberg M. and Tenson T. (2002) A new beginning of the end of translation. Nature Struct Biol 9(2):85-87

Heurgue-Hamard V, Champ S, Engstrom A, Ehrenberg M and Buckingham RH. (2002) The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors. EMBO J 21(4):769-778

Tenson T. and Ehrenberg M. (2002) Regulatory Nascent Peptides in the Ribosomal Tunnel. Cell 108(5):591-594

2001

Paulsson, J. and Ehrenberg, M. (2001) Sensitivity, fluctuations and energy costs in a minimal regulatory network: plasmid copy number control. Quart Rev Biophys 34(1):1-59.

Zavialov AV, Buckingham RH, Ehrenberg M. (2001) A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor rf3. Cell 107(1):115-24. link

Martinez J., Ren Y.G., Nilsson P., Ehrenberg M., Virtanen A. (2001) The mRNA cap structure stimulates rate of poly(A) removal and amplifies processivity of degradation. J Biol Chem 276(30):27923-9. link

Elf, J., Berg, O.G. & Ehrenberg, M. (2001) Comparison of repressor and transcriptional attenuator systems for control of amino acid biosynthetic operons. J Mol Biol 313(5):941-954

2000

Paulsson, J. and Ehrenberg, M. (2000) Molecular clocks reduce plasmid loss rates: the R1 case. J Mol Biol 297, 179-192

Freistroffer, D. V., Kwiatkowski, M., Buckingham, R.H. and Ehrenberg, M. (2000) The accuracy of termination by peptide release factors. Proc Natl Acad Sci USA 97, 2046-2051 pdf

Heurgué-Hamard, V., Dincbas, V., Buckingham, R. and Ehrenberg, M. (2000) Origins of minigene-dependent growth inhibition in bacterial cells. EMBO J 19, 2701-2709

Paulsson, J., Berg, O.G. and Ehrenberg, M. (2000) Stochastic Focusing: fluctuation-enhanced sensitivity of intracellular regulation. Proc Natl Acad Sci USA 97, 7148-7153 pdf

Paulsson, J. and Ehrenberg, M. (2000) Random signal-fluctuations can reduce random fluctuations in regulated components of chemical regulatory networks. Phys Rev Letters 84, 5447-5450

Nakamura, Y., Ito, K. and Ehrenberg, M. (2000) Mimicry grasps reality in translation termination. Cell 101, 349-52

Macvanin, C., Johansson, U., Ehrenberg, M. and Hughes, D. (2000) Fusidic acid resistant EF-G reduces the accumulation of (p)ppGpp. Mol Microbiol 37, 98-107

Berg, O.G., Paulsson, J. and Ehrenberg, M. (2000) Zero-order ultrasensitivity, fluctuations and quality of control in small systems. Biophysical J 79, 1228-1236

Berg, OG, Paulsson, J. and Ehrenberg, M. (2000) Fluctuations in Repressor Control: Thermodynamic Constraints on Stochastic Focusing. Biophysical J 79, 2944-2953

Dincbas-Renqvist, V., Engström, Å., Mora, L., Buckingham, R. and Ehrenberg, M. (2000) A post-translational modification in the GGQ motif of RF2 from E.coli stimulates termination translation. EMBO J 19, 6900-6907

Arkov, A.L., Freistroffer, D.V., Pavlov, M.Yu., Ehrenberg, M. and Murgola, E.J. (2000) Mutations in conserved regions of ribosomal RNAs decrease the productive association of peptide-chain release factors with the ribosome during translation termination. Biochimie 82(8):671-82.

1999

Karimi, R., Pavlov, M., Buckingham, RH and Ehrenberg, M. (1999) Novel roles for classical factors at the interface between translation termination and initiation. Molecular Cell 3, 601-609.

Karlsson, M., Pavlov, M.Y., Malmqvist, M., Persson, B. and Ehrenberg, M. (1999) Initiation of E.coli ribosomes on matrix coupled mRNAs studied by optical biosensor technique. Biochimie 81, 995-1002.

Liang, S.-T., Ehrenberg, M., Dennis, P. and Bremer, H. (1999) Decay of rplN and lacZ mRNA in Escherichia coli. J Mol Biol 288, 521-538.

Dincbas, V., Heurgué-Hamard, V., Buckingham, R. H., Karimi, R. and Ehrenberg, M. (1999) Shutdown in protein synthesis due to the expression of mini-genes in bacteria. J Mol Biol 291, 745-759.

Liang, S.-T., Bipatnath, M., Xu, Y.-C., Chen, S.-L., Dennis, P., Ehrenberg, M. and Bremer, H. (1999) Activities of constitutive promoters in Escherichia coli. J Mol Biol 292, 19-37.

1998

Heurgué-Hamard, V., Karimi, R., Mora, L., MacDougall, J., Leboeuf, C., Grentzmann, G., Ehrenberg, M. and Buckingham, R.H. (1998) Ribosome release factor RF4 and termination factor RF3 are involved in dissociation of peptidyl-tRNA from the ribosome. EMBO J 17, 808-816.

Arkov, A.L., Freistroffer, D. V., Ehrenberg, M. and Murgola, E.J. (1998) Mutations in RNAs of both ribosomal subunits cause defects in translation termination. EMBO J 17, 1507-1514.

Paulsson, J., Nordström K. and Ehrenberg, M. (1998) Requirements for rapid plasmid ColE1 copy number adjustments: A mathematical model of inhibition modes and RNA turnover rates. Plasmid 39, 215-234.

Paulsson, J. and Ehrenberg, M. (1998) Trade-off between segregational stability and metabolic burden: a mathematical model of plasmid CoIE1 replication control. J Mol Biol 279, 73-88.

Bilgin, N., Ehrenberg, M., Ebel, C., Zaccai, G., Sayers, Z., Koch, M.H., Svergun, D., Barberato, C., Volkov, V., Nissen, P. and Nyborg, J. (1998) Solution structure of the ternary complex between aminoacyl-tRNA, EF-Tu and guanosine triphosphate. Biochemistry 37, 8163-8172.

Karimi, R., Pavlov, M.Y., Buckingham, R.H. and Ehrenberg, M. (1998) Initiation factors IF1 and IF2 synergistically remove small peptidyl-tRNAs from E.coli ribosomes. J Mol Biol 281, 241-252.

Bilgin N. and Ehrenberg, M. (1998) Measurement of rate of protein synthesis in vitro. Preparation of Escherichia coli burst systems. Methods Mol Biol. 77, 243-256.

Ehrenberg M. and Bilgin, N. (1998) Measurement of ribosomal accuracy and proofreading in E. coli burst systems. Methods Mol Biol 77:227-241.

Pavlov, M.Yu., Freistroffer, D., Dincbas, V., MacDougall, J., Buckingham, R. and Ehrenberg, M. (1998) A direct estimation of the context effect on the efficiency of termination. J Mol Biol. 284, 579-590.

1997

Randall, L.L., Topping, T.B., Hardy, J.S., Pavlov, M.Y., Freistroffer, D. and Ehrenberg, M. (1997) Interaction of SecB with nascent and with full-length, denatured polypeptides: the same parameters govern binding. Proc Natl Acad Sci USA 94, 802-807.

Pavlov, Y.M., Freistroffer, F., Buckingham, R., MacDougall, J. and Ehrenberg, M. (1997) Fast recycling of E.coli ribosomes requires both RF3 and RRF. EMBO J 16, 4134-4141.

Freistroffer, D., Pavlov, M., Buckingham, MacDougall, J. and Ehrenberg, M. (1997) RF3 accelerates the recycling of RF1 and RF2 in a GTP-dependent way. EMBO J 16, 4126-4133.

Pavlov, M., Freistroffer, D. and Ehrenberg, M. (1997) Synthesis of region labelled proteins for NMR studies by in-vitro translation of column coupled mRNAs. Biochimie 79, 415-422.

Saarma, U., Remme, J., Ehrenberg, M. and Bilgin, N. (1997) An A to U transversion at position 1067 of 23 S rRNA from Escherichia coli impairs EF-Tu and EF-G function. J Mol Biol 272, 327-335.

Pavlov, M.Y., Freistroffer, D., Buckingham, R. and Ehrenberg, M. (1997) Release factor RF3 abolishes competition between release factor RF1 and ribosome recycling factor, RRF, for a ribosome binding site. J Mol Biol 273, 389-401.

McDougall, J., Holst-Hansen, P., Mortensen, K.K., Freistroffer, D.V., Pavlov, M.Y., Ehrenberg, M. and Buckingham, R. H. (1997) Purification of active Escherichia coli ribosome recycling factor, RRF, from an osmo-regulated expression system. Biochimie 79, 243-246.

1996

Ehrenberg, M. (1996) Hypothesis: Hypersensitive plasmid copy number control for ColE1. Biophysical J 70, 135-145.

Karimi, R. and Ehrenberg, M. (1996) Dissociation rates of dipeptidyl-tRNA from the P-site of E.coli ribosomes. EMBO J 15, 1149-1154.

Pavlov, M. and Ehrenberg, M. (1996) Rate of translation of natural mRNAs in an optimized in vitro translation system. Arch Bioch Biophys 328, 9-16.

Abdulkarim, F., Ehrenberg, M. and Hughes, D. (1996) Mutants of EF-Tu defective in binding aminoacyl-tRNA. FEBS Letters 382, 297-303.

1995

Ehrenberg, M., Bilgin, N., Dincbas, V., Karimi, R., Hughes, D. and Abdulkarim, F. (1995) tRNA-ribosome interactions. Biochem Cell Biol 73, 1049-1054.

Dincbas, V., Bilgin, N., Scoble, J. and Ehrenberg, M. (1995). Two GTP's are consumed per peptide bond in poly(Phe)-synthesis, in spite of switching stoichiometry of the EF-Tu.aminoacyl-tRNA complex with temperature. FEBS Letters 357, 19-22.

Bilgin N. and Ehrenberg, M. (1995). The stoichiometry between EF-Tu.GTP and aminoacyl-tRNA switches with temperature. Biochemistry 34, 715-719.

Bremer, H., and Ehrenberg, M. (1995). Guanosine tetraphosphate as a global regulator of bacterial RNA synthesis: A new model involving RNA polymerase pausing and queuing. Bioch and Biophys Acta 1262, 15-36.

Ehrenberg, M. and Sverredal, A. (1995). A model for copy number control of the plasmid R1. J Mol Biol 246, 472-485.

Alexander C, Bilgin N, Lindschau C, Mesters JR, Kraal B, Hilgenfeld R, Erdmann VA, Lippmann C (1995) Phosphorylation of elongation factor Tu prevents ternary complex formation. J Biol Chem 270, 14541-7.

1994

Bilgin, N. and Ehrenberg, M. (1994). Mutations in 23S ribosomal RNA perturb transfer RNA selection and can lead to streptomycin dependence. J Mol Biol 235, 813-824.

Scoble, J., Bilgin, N., & Ehrenberg, M. (1994). Two GTP's are hydrolyzed on two molecules of EF-Tu for each elongation cycle during code translation. Biochimie 76, 59-62.

Karimi, R. and Ehrenberg, M. (1994). Dissociation rate of cognate peptidyl-tRNA from the A-site of hyper-accurate and error-prone ribosomes. Eur J Biochem 226, 355-360.

Weiser J, Ehrenberg M, Naprstek J (1994) In vitro measurement of translation accuracy of ribosomes isolated from streptomycin-resistant mutant of Streptomyces granaticolor. Folia Microbiol (Praha) 39, 129-132.

Monographs

Kurland, C.G., Hughes, D. and Ehrenberg, M. (1996). Limitations in translational accuracy. In Escherichia coli and Salmonella. Ed. F.C. Neidhardt. ASM Press. pp 979-1004.

Ehrenberg, M., Dincbas, V., Freistroffer, D., Heurgué-Hamard, V., Karimi, R., Pavlov, M. and Buckingham, R. H. (2000) The mechanism of prokaryotic translation termination and ribosome recycling. In The Ribosome (Garret, R.&al., eds.). A.S.M. Press, Washington, D.C.