Protocol for intervention-free quantification of protein turnover rate by steady-state modeling

Stefania Marcotti; Besaiz Sánchez Sánchez; Eduardo Serna Morales; Anca Dragu; María-del-Carmen Díaz-de-la-Loza; Yutaka Matsubayashi; Brian Stramer

doi:10.1016/j.xpro.2021.100377

Protocol for intervention-free quantification of protein turnover rate by steady-state modeling

Stefania Marcotti, Besaiz Sánchez Sánchez, Eduardo Serna Morales, Anca Dragu, María-del-Carmen Díaz-de-la-Loza, Yutaka Matsubayashi, Brian Stramer

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Abstract

Protein turnover rate is difficult to obtain experimentally. This protocol shows how to mathematically model turnover rates in an intervention-free manner given the ability to quantify mRNA and protein expression from initiation to homeostasis. This approach can be used to calculate production and degradation rates and to infer protein half-life. This model was successfully employed to quantify turnover during Drosophila embryogenesis, and we hypothesize that it will be applicable to diverse in vivo or in vitro systems.

Original language	English
Article number	100377
Journal	STAR Protocols
Volume	2
Issue number	1
DOIs	https://doi.org/10.1016/j.xpro.2021.100377
Publication status	Published - 19 Mar 2021

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title = "Protocol for intervention-free quantification of protein turnover rate by steady-state modeling",

abstract = "Protein turnover rate is difficult to obtain experimentally. This protocol shows how to mathematically model turnover rates in an intervention-free manner given the ability to quantify mRNA and protein expression from initiation to homeostasis. This approach can be used to calculate production and degradation rates and to infer protein half-life. This model was successfully employed to quantify turnover during Drosophila embryogenesis, and we hypothesize that it will be applicable to diverse in vivo or in vitro systems.",

author = "Stefania Marcotti and {S{\'a}nchez S{\'a}nchez}, Besaiz and {Serna Morales}, Eduardo and Anca Dragu and Mar{\'i}a-del-Carmen D{\'i}az-de-la-Loza and Yutaka Matsubayashi and Brian Stramer",

note = "Funding Information: This project has been funded from the Wellcome Trust (grant no. 107859/Z/15/Z) and the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement no. 681808). Conceptualization and Methodology, B.J.S.-S. Y.M. and B.M.S.; Software, S.M.; Formal Analysis and Data Curation, S.M. B.J.S.-S. E.S.-M. and Y.M.; Investigation, B.J.S.-S. E.S.-M. A.D. M.D.C.D.D.L.L. and Y.M.; Writing ? Original Draft, S.M.; Writing ? Review & Editing, S.M. B.J.S.-S. E.S.-M. M.D.C.D.D.L.L. Y.M. and B.M.S.; Funding Acquisition and Supervision, B.M.S. The authors declare no competing interests. Publisher Copyright: {\textcopyright} 2021 The Author(s) Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

year = "2021",

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doi = "10.1016/j.xpro.2021.100377",

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AU - Marcotti, Stefania

AU - Sánchez Sánchez, Besaiz

AU - Serna Morales, Eduardo

AU - Dragu, Anca

AU - Díaz-de-la-Loza, María-del-Carmen

AU - Matsubayashi, Yutaka

AU - Stramer, Brian

N1 - Funding Information: This project has been funded from the Wellcome Trust (grant no. 107859/Z/15/Z) and the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement no. 681808). Conceptualization and Methodology, B.J.S.-S. Y.M. and B.M.S.; Software, S.M.; Formal Analysis and Data Curation, S.M. B.J.S.-S. E.S.-M. and Y.M.; Investigation, B.J.S.-S. E.S.-M. A.D. M.D.C.D.D.L.L. and Y.M.; Writing ? Original Draft, S.M.; Writing ? Review & Editing, S.M. B.J.S.-S. E.S.-M. M.D.C.D.D.L.L. Y.M. and B.M.S.; Funding Acquisition and Supervision, B.M.S. The authors declare no competing interests. Publisher Copyright: © 2021 The Author(s) Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2021/3/19

Y1 - 2021/3/19

N2 - Protein turnover rate is difficult to obtain experimentally. This protocol shows how to mathematically model turnover rates in an intervention-free manner given the ability to quantify mRNA and protein expression from initiation to homeostasis. This approach can be used to calculate production and degradation rates and to infer protein half-life. This model was successfully employed to quantify turnover during Drosophila embryogenesis, and we hypothesize that it will be applicable to diverse in vivo or in vitro systems.

AB - Protein turnover rate is difficult to obtain experimentally. This protocol shows how to mathematically model turnover rates in an intervention-free manner given the ability to quantify mRNA and protein expression from initiation to homeostasis. This approach can be used to calculate production and degradation rates and to infer protein half-life. This model was successfully employed to quantify turnover during Drosophila embryogenesis, and we hypothesize that it will be applicable to diverse in vivo or in vitro systems.

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Protocol for intervention-free quantification of protein turnover rate by steady-state modeling

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