{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:21:43Z","timestamp":1772173303350,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1011918","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,3,15]],"date-time":"2024-03-15T00:00:00Z","timestamp":1710460800000}}],"reference-count":50,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2024,3,5]],"date-time":"2024-03-05T00:00:00Z","timestamp":1709596800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["437345987"],"award-info":[{"award-number":["437345987"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008662","name":"Joachim Herz Stiftung","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008662","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Processive enzymes like polymerases or ribosomes are often studied in bulk experiments by monitoring time-dependent signals, such as fluorescence time traces. However, due to biomolecular process stochasticity, ensemble signals may lack the distinct features of single-molecule signals. Here, we demonstrate that, under certain conditions, bulk signals from processive reactions can be decomposed to unveil hidden information about individual reaction steps. Using mRNA translation as a case study, we show that decomposing a noisy ensemble signal generated by the translation of mRNAs with more than a few codons is an ill-posed problem, addressable through Tikhonov regularization. We apply our method to the fluorescence signatures of\n                    <jats:italic>in-vitro<\/jats:italic>\n                    translated LepB mRNA and determine codon-position dependent translation rates and corresponding state-specific fluorescence intensities. We find a significant change in fluorescence intensity after the fourth and the fifth peptide bond formation, and show that both codon position and encoded amino acid have an effect on the elongation rate. This demonstrates that our approach enhances the information content extracted from bulk experiments, thereby expanding the range of these time- and cost-efficient methods.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1011918","type":"journal-article","created":{"date-parts":[[2024,3,5]],"date-time":"2024-03-05T13:30:09Z","timestamp":1709645409000},"page":"e1011918","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Decomposing bulk signals to reveal hidden information in processive enzyme reactions: A case study in mRNA translation"],"prefix":"10.1371","volume":"20","author":[{"given":"Nadin","family":"Haase","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wolf","family":"Holtkamp","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simon","family":"Christ","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dag","family":"Heinemann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marina V.","family":"Rodnina","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7653-3733","authenticated-orcid":true,"given":"Sophia","family":"Rudorf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2024,3,5]]},"reference":[{"issue":"9","key":"pcbi.1011918.ref001","doi-asserted-by":"crossref","first-page":"1699","DOI":"10.1110\/ps.10301","article-title":"A structural basis for processivity","volume":"10","author":"WA Breyer","year":"2001","journal-title":"Protein Sci"},{"key":"pcbi.1011918.ref002","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1111\/j.1749-6632.1994.tb52803.x","article-title":"On the processivity of polymerases","volume":"726","author":"PHV Hippel","year":"1994","journal-title":"Ann N Y Acad Sci"},{"key":"pcbi.1011918.ref003","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.jpba.2015.01.042","article-title":"Analytical methods for kinetic studies of biological interactions: A review","volume":"113","author":"X Zheng","year":"2015","journal-title":"J Pharm Biomed Anal"},{"key":"pcbi.1011918.ref004","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1038\/nchembio0808-440","article-title":"Cutting the forest to see a single tree?","volume":"4","author":"A van Oijen","year":"2008","journal-title":"Nature chemical biology"},{"issue":"1","key":"pcbi.1011918.ref005","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1021\/acschembio.9b00619","article-title":"Processivity in Bacterial Glycosyltransferases","volume":"15","author":"L Yakovlieva","year":"2020","journal-title":"ACS Chem Biol"},{"issue":"12","key":"pcbi.1011918.ref006","doi-asserted-by":"crossref","first-page":"1205","DOI":"10.1101\/gad.2050011","article-title":"Biological mechanisms, one molecule at a time","volume":"25","author":"I T","year":"2011","journal-title":"Genes Dev"},{"key":"pcbi.1011918.ref007","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.ymeth.2017.12.007","article-title":"Ensemble and single-molecule FRET studies of protein synthesis","volume":"137","author":"WC Lai","year":"2018","journal-title":"Methods"},{"issue":"22","key":"pcbi.1011918.ref008","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gky1101","article-title":"Decomposition of time-dependent fluorescence signals reveals codon-specific kinetics of protein synthesis","volume":"46","author":"N Haase","year":"2018","journal-title":"Nucleic Acids Research"},{"issue":"10","key":"pcbi.1011918.ref009","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.0030189","article-title":"Universally sloppy parameter sensitivities in systems biology models","volume":"3","author":"RN Gutenkunst","year":"2007","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"pcbi.1011918.ref010","doi-asserted-by":"crossref","first-page":"e1000696","DOI":"10.1371\/journal.pcbi.1000696","article-title":"Parameter estimation and model selection in computational biology","volume":"6","author":"G Lillacci","year":"2010","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"pcbi.1011918.ref011","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/s13068-021-01922-0","article-title":"Current and future advances in fluorescence-based visualization of plant cell wall components and cell wall biosynthetic machineries","volume":"14","author":"BT DeVree","year":"2021","journal-title":"Biotechnology for Biofuels"},{"issue":"39","key":"pcbi.1011918.ref012","article-title":"Single-molecule localization microscopy","volume":"1","author":"M Lelek","year":"2021","journal-title":"Nature Reviews Methods Primers"},{"issue":"1","key":"pcbi.1011918.ref013","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.ab.2009.04.035","article-title":"A quantitative stopped-flow fluorescence assay for measuring polymerase elongation rates","volume":"391","author":"P Gong","year":"2009","journal-title":"Anal Biochem"},{"issue":"52","key":"pcbi.1011918.ref014","doi-asserted-by":"crossref","first-page":"13691","DOI":"10.1073\/pnas.1719592115","article-title":"Three tRNAs on the ribosome slow translation elongation","volume":"114","author":"J Choi","year":"2017","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"18","key":"pcbi.1011918.ref015","doi-asserted-by":"crossref","first-page":"10201","DOI":"10.1093\/nar\/gkac576","article-title":"Uncovering translation roadblocks during the development of a synthetic tRNA","volume":"50","author":"A Prabhakar","year":"2022","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"pcbi.1011918.ref016","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1080\/05704928.2017.1376680","article-title":"Fluorophore tagged bio-molecules and their applications: A brief review","volume":"53","author":"I Sarkar","year":"2018","journal-title":"Applied Spectroscopy Reviews"},{"issue":"12","key":"pcbi.1011918.ref017","doi-asserted-by":"crossref","first-page":"1443","DOI":"10.1038\/s41557-022-01039-3","article-title":"Synthesis and single-molecule imaging reveal stereospecific enhancement of binding kinetics by the antitumour eEF1A antagonist SR-A3","volume":"14","author":"HY Wang","year":"2022","journal-title":"Nature Chemistry"},{"issue":"4","key":"pcbi.1011918.ref018","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1038\/s41592-021-01081-y","article-title":"Single-molecule FRET imaging of GPCR dimers in living cells","volume":"18","author":"WB Asher","year":"2021","journal-title":"Nature Methods"},{"key":"pcbi.1011918.ref019","article-title":"mTORC1 Enhances Early Phase Ribosome Processivity","volume":"7","author":"E An","year":"2020","journal-title":"Frontiers in Molecular Biosciences"},{"issue":"6","key":"pcbi.1011918.ref020","doi-asserted-by":"crossref","first-page":"2528","DOI":"10.1093\/nar\/gkw137","article-title":"Quantitative assessment of ribosome drop-off in E. coli","volume":"44","author":"C Sin","year":"2016","journal-title":"Nucleic acids research"},{"issue":"1","key":"pcbi.1011918.ref021","doi-asserted-by":"crossref","first-page":"e02143","DOI":"10.1128\/mBio.02143-17","article-title":"Simultaneous Binding of Multiple EF-Tu Copies to Translating Ribosomes in Live Escherichia coli","volume":"9","author":"M Mustafi","year":"2018","journal-title":"mBio"},{"issue":"1","key":"pcbi.1011918.ref022","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1111\/j.1365-2958.2012.08081.x","article-title":"Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells","volume":"85","author":"S Bakshi","year":"2012","journal-title":"Mol Microbiol"},{"issue":"1","key":"pcbi.1011918.ref023","doi-asserted-by":"crossref","first-page":"1852","DOI":"10.1038\/s41467-022-29515-x","article-title":"Direct measurements of mRNA translation kinetics in living cells","volume":"13","author":"M Metelev","year":"2022","journal-title":"Nature Communications"},{"issue":"3","key":"pcbi.1011918.ref024","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2014.09.039","article-title":"A protein tagging system for signal amplification in gene expression and fluorescence imaging","volume":"159","author":"ME Tanenbaum","year":"2015","journal-title":"Cell"},{"issue":"11","key":"pcbi.1011918.ref025","doi-asserted-by":"crossref","first-page":"a032078","DOI":"10.1101\/cshperspect.a032078","article-title":"Quantifying Single mRNA Translation Kinetics in Living Cells","volume":"10","author":"T Morisaki","year":"2018","journal-title":"Cold Spring Harb Perspect Biol"},{"issue":"4","key":"pcbi.1011918.ref026","doi-asserted-by":"crossref","first-page":"990","DOI":"10.1016\/j.cell.2016.04.040","article-title":"Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells","volume":"165","author":"C Wang","year":"2016","journal-title":"Cell"},{"key":"pcbi.1011918.ref027","doi-asserted-by":"crossref","unstructured":"Hansen C. Rank-Deficient and Discrete Ill-Posed Problems: Numerical Aspects of Linear Inversion (Monographs on Mathematical Modeling and Computation). Society for Industrial and Applied Mathematics; 1998.","DOI":"10.1137\/1.9780898719697"},{"issue":"1","key":"pcbi.1011918.ref028","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1137\/S0895479897326432","article-title":"Tikhonov Regularization And Total Least Squares","volume":"21","author":"GH Golub","year":"1999","journal-title":"SIAM Journal on Matrix Analysis and Applications"},{"issue":"3","key":"pcbi.1011918.ref029","doi-asserted-by":"crossref","DOI":"10.1216\/JIE-2010-22-3-465","article-title":"An iterative method for Tikhonov regularization with a general linear regularization operator","volume":"22","author":"ME Hochstenbach","year":"2010","journal-title":"Journal of Integral Equations and Applications"},{"issue":"3","key":"pcbi.1011918.ref030","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1137\/S1064827593252672","article-title":"A Regularization Parameter in Discrete Ill-Posed Problems","volume":"17","author":"T Regi\u0144ska","year":"1996","journal-title":"Siam Journal on Scientific Computing"},{"issue":"7","key":"pcbi.1011918.ref031","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1101\/gr.257741.119","article-title":"Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing","volume":"30","author":"AB Arpat","year":"2020","journal-title":"Genome Res"},{"issue":"4","key":"pcbi.1011918.ref032","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1016\/j.febslet.2004.10.105","article-title":"The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl transfer","volume":"579","author":"J Frank","year":"2005","journal-title":"FEBS Lett"},{"issue":"1","key":"pcbi.1011918.ref033","article-title":"MATHEMATICAL AND COMPUTATIONAL MODELLING OF RIBOSOMAL MOVEMENT AND PROTEIN SYNTHESIS: AN OVERVIEW","volume":"1","author":"T v d Haar","year":"2012","journal-title":"Computational and Structural Biotechnology Journal"},{"issue":"52","key":"pcbi.1011918.ref034","doi-asserted-by":"crossref","DOI":"10.1021\/ja510082j","article-title":"Timing Is Everything: Unifying Codon Translation Rates and Nascent Proteome Behavior","volume":"136","author":"D Nissley","year":"2014","journal-title":"Journal of the American Chemical Society"},{"issue":"2","key":"pcbi.1011918.ref035","doi-asserted-by":"crossref","first-page":"e1007618","DOI":"10.1371\/journal.pcbi.1007618","article-title":"A stochastic model for simulating ribosome kinetics in vivo","volume":"16","author":"EC Dykeman","year":"2020","journal-title":"PLoS Comput Biol"},{"issue":"2","key":"pcbi.1011918.ref036","doi-asserted-by":"crossref","first-page":"e1010870","DOI":"10.1371\/journal.pcbi.1010870","article-title":"Modelling ribosome kinetics and translational control on dynamic mRNA","volume":"19","author":"EC Dykeman","year":"2023","journal-title":"PLoS Comput Biol"},{"issue":"10","key":"pcbi.1011918.ref037","doi-asserted-by":"crossref","first-page":"e1003909","DOI":"10.1371\/journal.pcbi.1003909","article-title":"Deducing the Kinetics of Protein Synthesis In Vivo from the Transition Rates Measured In Vitro","volume":"10","author":"S Rudorf","year":"2014","journal-title":"PLoS Computational Biology"},{"issue":"8","key":"pcbi.1011918.ref038","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0134994","article-title":"Protein Synthesis in E. coli: Dependence of Codon-Specific Elongation on tRNA Concentration and Codon Usage","volume":"10","author":"S Rudorf","year":"2015","journal-title":"PLOS ONE"},{"issue":"45","key":"pcbi.1011918.ref039","doi-asserted-by":"crossref","first-page":"17031","DOI":"10.1021\/ja407511q","article-title":"A Kinetic Safety Gate Controlling the Delivery of Unnatural Amino Acids to the Ribosome","volume":"135","author":"J Mittelstaet","year":"2013","journal-title":"Journal of the American Chemical Society"},{"key":"pcbi.1011918.ref040","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1038\/nature09206","article-title":"Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy","volume":"466","author":"N Fischer","year":"2010","journal-title":"Nature"},{"issue":"42","key":"pcbi.1011918.ref041","doi-asserted-by":"crossref","first-page":"12767","DOI":"10.1021\/bi061192z","article-title":"Delayed Release of Inorganic Phosphate from Elongation Factor Tu Following GTP Hydrolysis on the Ribosome","volume":"45","author":"U Kothe","year":"2006","journal-title":"Biochemistry"},{"issue":"3","key":"pcbi.1011918.ref042","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/j.molcel.2005.12.018","article-title":"A Uniform Response to Mismatches in Codon-Anticodon Complexes Ensures Ribosomal Fidelity","volume":"21","author":"KB Gromadski","year":"2006","journal-title":"Molecular cell"},{"issue":"2","key":"pcbi.1011918.ref043","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/S1097-2765(04)00005-X","article-title":"Kinetic Determinants of High-Fidelity tRNA Discrimination on the Ribosome","volume":"13","author":"KB Gromadski","year":"2004","journal-title":"Molecular cell"},{"issue":"24","key":"pcbi.1011918.ref044","doi-asserted-by":"crossref","first-page":"7490","DOI":"10.1093\/emboj\/17.24.7490","article-title":"Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E.coli ribosome","volume":"17","author":"T Pape","year":"1998","journal-title":"The EMBO Journal"},{"issue":"2","key":"pcbi.1011918.ref045","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1074\/jbc.271.2.646","article-title":"Initial Binding of the Elongation Factor Tu-GTP-Aminoacyl-tRNA Complex Preceding Codon Recognition on the Ribosome","volume":"271","author":"MV Rodnina","year":"1996","journal-title":"Journal of Biological Chemistry"},{"key":"pcbi.1011918.ref046","volume-title":"An introduction to stochastic modeling","author":"HM Taylor","year":"1985"},{"issue":"4459","key":"pcbi.1011918.ref047","article-title":"High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide","volume":"5","author":"E Samatova","year":"2014","journal-title":"Nat Commun"},{"issue":"6","key":"pcbi.1011918.ref048","doi-asserted-by":"crossref","first-page":"1945","DOI":"10.1073\/pnas.92.6.1945","article-title":"GTP consumption of elongation factor Tu during translation of heteropolymeric mRNAs","volume":"92","author":"MV Rodnina","year":"1995","journal-title":"PNAS"},{"issue":"1","key":"pcbi.1011918.ref049","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1137\/141000671","article-title":"Julia: A Fresh Approach to Numerical Computing","volume":"59","author":"J Bezanson","year":"2017","journal-title":"SIAM Review"},{"issue":"1","key":"pcbi.1011918.ref050","first-page":"5","article-title":"Plots.Jl\u2014A User Extendable Plotting API for the Julia Programming Language","volume":"11","author":"S Christ","year":"2023","journal-title":"Ubiquity Press"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1011918","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,3,15]],"date-time":"2024-03-15T00:00:00Z","timestamp":1710460800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1011918","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,15]],"date-time":"2024-03-15T13:58:09Z","timestamp":1710511089000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1011918"}},"subtitle":[],"editor":[{"given":"Stefan","family":"Klumpp","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,3,5]]},"references-count":50,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2024,3,5]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1011918","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.05.17.541147","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,3,5]]}}}