{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T10:49:40Z","timestamp":1761648580447,"version":"build-2065373602"},"reference-count":39,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2018,10,14]],"date-time":"2018-10-14T00:00:00Z","timestamp":1539475200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Data"],"abstract":"<jats:p>Protein synthesis is at the core of bottom-up construction of artificial cellular mimics. Intriguingly, several reports have revealed that when a transcription\u2013translation (TX\u2013TL) kit is encapsulated inside lipid vesicles (or water-in-oil droplets), high between-vesicles diversity is observed in terms of protein synthesis rate and yield. Stochastic solute partition can be a major determinant of these observations. In order to verify that the variation of TX\u2013TL components concentration brings about a variation of produced protein rate and yield, here we directly measure the performances of the \u2018PURE system\u2019 TX\u2013TL kit variants. We report and share the kinetic traces of the enhanced Green Fluorescent Protein (eGFP) synthesis in bulk aqueous phase, for 27 combinatorial block-variants. The eGFP production is a sensitive function of TX\u2013TL components concentration in the explored concentration range. Providing direct evidence that protein synthesis yield and rate actually mirror the TX\u2013TL composition, this study supports the above-mentioned hypothesis on stochastic solute partition, without excluding, however, the contribution of other factors (e.g., inactivation of components).<\/jats:p>","DOI":"10.3390\/data3040041","type":"journal-article","created":{"date-parts":[[2018,10,15]],"date-time":"2018-10-15T03:43:01Z","timestamp":1539574981000},"page":"41","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Measurement and Numerical Modeling of Cell-Free Protein Synthesis: Combinatorial Block-Variants of the PURE System"],"prefix":"10.3390","volume":"3","author":[{"given":"Paolo","family":"Carrara","sequence":"first","affiliation":[{"name":"Sciences Department, Roma Tre University, V.le G. Marconi 446, I-00146 Rome, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3171-6645","authenticated-orcid":false,"given":"Emiliano","family":"Altamura","sequence":"additional","affiliation":[{"name":"Chemistry Department, University of Bari \u201cAldo Moro\u201d, Via Orabona 4, I-70125 Bari, Italy"}]},{"given":"Francesca","family":"D\u2019Angelo","sequence":"additional","affiliation":[{"name":"Sciences Department, Roma Tre University, V.le G. Marconi 446, I-00146 Rome, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0299-0012","authenticated-orcid":false,"given":"Fabio","family":"Mavelli","sequence":"additional","affiliation":[{"name":"Chemistry Department, University of Bari \u201cAldo Moro\u201d, Via Orabona 4, I-70125 Bari, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2228-2825","authenticated-orcid":false,"given":"Pasquale","family":"Stano","sequence":"additional","affiliation":[{"name":"Sciences Department, Roma Tre University, V.le G. Marconi 446, I-00146 Rome, Italy"},{"name":"DiSTeBA, University of Salento, Ecotekne, I-73100 Lecce, Italy"}]}],"member":"1968","published-online":{"date-parts":[[2018,10,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1002\/ar.10155","article-title":"Toward the engineering of minimal living cells","volume":"268","author":"Luisi","year":"2002","journal-title":"Anat. Rec."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/S0167-7799(02)01909-1","article-title":"Artificial cells: Prospects for biotechnology","volume":"20","author":"Pohorille","year":"2002","journal-title":"Trends Biotechnol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00114-005-0056-z","article-title":"Approaches to semi-synthetic minimal cells: A review","volume":"93","author":"Luisi","year":"2006","journal-title":"Naturwissenschaften"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1101\/sqb.2009.74.014","article-title":"Reconstructing the emergence of cellular life through the synthesis of model protocells","volume":"74","author":"Mansy","year":"2009","journal-title":"Cold Spring Harbor Symp. Quant. Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"a004945","DOI":"10.1101\/cshperspect.a004945","article-title":"Constructing partial models of cells","volume":"2","author":"Ichihashi","year":"2010","journal-title":"Cold Spring Harbor Perspect. Biol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1038\/nchem.1127","article-title":"Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA","volume":"3","author":"Kurihara","year":"2011","journal-title":"Nat. Chem."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"3114","DOI":"10.1002\/anie.201107123","article-title":"Triggered gene expression in fed-vesicle microreactors with a multifunctional membrane","volume":"51","author":"Nourian","year":"2012","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1146\/annurev-biochem-080411-124036","article-title":"Progress Toward Synthetic Cells","volume":"83","author":"Blain","year":"2014","journal-title":"Annu. Rev. Biochem."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1007\/BF01808123","article-title":"Self-replicating micelles\u2014A chemical version of a minimal autopoietic system","volume":"19","author":"Luisi","year":"1989","journal-title":"Origins Life Evol. Biosphere"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/357057a0","article-title":"Autocatalytic Self-Replicating Micelles as Models for Prebiotic Structures","volume":"357","author":"Bachmann","year":"1992","journal-title":"Nature"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1006\/bbrc.1995.1180","article-title":"Enzymatic RNA replication in self-reproducing vesicles: An approach to a minimal cell","volume":"207","author":"Oberholzer","year":"1995","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1700","DOI":"10.3390\/life5041700","article-title":"Protocells Models in Origin of Life and Synthetic Biology","volume":"5","author":"Stano","year":"2015","journal-title":"Life"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1006\/bbrc.1999.0404","article-title":"Protein expression in liposomes","volume":"261","author":"Oberholzer","year":"1999","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1016\/S1389-1723(01)80322-4","article-title":"Synthesis of functional protein in liposome","volume":"92","author":"Yu","year":"2001","journal-title":"J. Biosci. Bioeng."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"18887","DOI":"10.1039\/c1jm12298c","article-title":"Compartmentalized reactions as a case of soft-matter biotechnology: Synthesis of proteins and nucleic acids inside lipid vesicles","volume":"21","author":"Stano","year":"2011","journal-title":"J. Mater. Chem."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"ysy011","DOI":"10.1093\/synbio\/ysy011","article-title":"Extrinsic stochastic factors (solute partition) in gene expression inside lipid vesicles and lipid-stabilized water-in-oil droplets: A review","volume":"3","author":"Altamura","year":"2018","journal-title":"Synth. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1162\/ARTL_a_00187","article-title":"Experiments on and Numerical Modeling of the Capture and Concentration of Transcription\u2013translation Machinery inside Vesicles","volume":"21","author":"Mavelli","year":"2015","journal-title":"Artif. Life"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Paradisi, P., Allegrini, P., and Chiarugi, D. (2015). A renewal model for the emergence of anomalous solute crowding in liposomes. BMC Syst. Biol., 9.","DOI":"10.1186\/1752-0509-9-S3-S7"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1038\/90802","article-title":"Cell-free translation reconstituted with purified components","volume":"19","author":"Shimizu","year":"2001","journal-title":"Nat. Biotechnol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/j.ymeth.2005.04.006","article-title":"Protein synthesis by pure translation systems","volume":"36","author":"Shimizu","year":"2005","journal-title":"Methods"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.ab.2006.06.040","article-title":"Femtoliter compartment in liposomes for in vitro selection of proteins","volume":"357","author":"Sunami","year":"2006","journal-title":"Anal. Biochem."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.bbrc.2007.07.201","article-title":"Protein synthesis in liposomes with a minimal set of enzymes","volume":"363","author":"Murtas","year":"2007","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1038\/nchem.1869","article-title":"Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator","volume":"6","author":"Weitz","year":"2014","journal-title":"Nat. Chem."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1006\/jmbi.1996.0428","article-title":"Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates","volume":"260","author":"Dong","year":"1996","journal-title":"J. Mol. Biol."},{"key":"ref_25","first-page":"179","article-title":"Giant Vesicles and w\/o Emulsions as Biochemical Reactors","volume":"39","author":"Carrara","year":"2008","journal-title":"Orig. Life Evol. Biosph."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1021\/sb400203p","article-title":"Gene circuit performance characterization and resource usage in a cell-free \u201cbreadboard\u201d","volume":"3","author":"Tuza","year":"2014","journal-title":"ACS Synth. Biol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.ymeth.2015.05.020","article-title":"Characterizing and prototyping genetic networks with cell-free transcription\u2013translation reactions","volume":"86","author":"Takahashi","year":"2015","journal-title":"Methods"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1021\/acssynbio.5b00296","article-title":"The All E. coli TX\u2013TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology","volume":"5","author":"Garamella","year":"2016","journal-title":"ACS Synth. Biol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"13397","DOI":"10.1002\/anie.201306613","article-title":"A remarkable self-organization process as the origin of primitive functional cells","volume":"52","author":"Stano","year":"2013","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1007\/s11538-015-0082-8","article-title":"A Simple Protein Synthesis Model for the PURE System Operation","volume":"77","author":"Mavelli","year":"2015","journal-title":"Bull. Math. Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1039\/c2ib00102k","article-title":"Experiment and mathematical modeling of gene expression dynamics in a cell-free system","volume":"4","author":"Windhager","year":"2012","journal-title":"Integr. Biol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1038\/msb.2009.50","article-title":"Quantifying epistatic interactions among the components constituting the protein translation system","volume":"5","author":"Matsuura","year":"2009","journal-title":"Mol. Syst. Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1002\/1439-7633(20020503)3:5<409::AID-CBIC409>3.0.CO;2-P","article-title":"Giant vesicles as microreactors for enzymatic mRNA synthesis","volume":"3","author":"Fischer","year":"2002","journal-title":"ChemBioChem"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2073","DOI":"10.1002\/cbic.201500274","article-title":"Protein Synthesis in Sub-Micrometer Water-in-Oil Droplets","volume":"16","author":"Gallo","year":"2015","journal-title":"ChemBioChem"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.1002\/cbic.200700112","article-title":"Lecithin-based water-in-oil compartments as dividing bioreactors","volume":"8","author":"Fiordemondo","year":"2007","journal-title":"ChemBioChem"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH Image to ImageJ: 25 years of image analysis","volume":"9","author":"Schneider","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1002\/cbic.200800810","article-title":"The minimal size of liposome-based model cells brings about a remarkably enhanced entrapment and protein synthesis","volume":"10","author":"Stano","year":"2009","journal-title":"ChemBioChem"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/j.ab.2011.03.036","article-title":"Kinetic study of de novo chromophore maturation of fluorescent proteins","volume":"414","author":"Iizuka","year":"2011","journal-title":"Anal. Biochem."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/j.ab.2011.10.040","article-title":"Chromophore maturation and fluorescence fluctuation spectroscopy of fluorescent proteins in a cell-free expression system","volume":"421","author":"Macdonald","year":"2012","journal-title":"Anal. Biochem."}],"container-title":["Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-5729\/3\/4\/41\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T15:25:31Z","timestamp":1760196331000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-5729\/3\/4\/41"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,10,14]]},"references-count":39,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2018,12]]}},"alternative-id":["data3040041"],"URL":"https:\/\/doi.org\/10.3390\/data3040041","relation":{},"ISSN":["2306-5729"],"issn-type":[{"type":"electronic","value":"2306-5729"}],"subject":[],"published":{"date-parts":[[2018,10,14]]}}}