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. For complete details on the use and execution of this protocol, please refer to Matsubayashi et al. (2020).

Keywords: Bioinformatics; Cell biology; Model organisms; Molecular biology; Protein biochemistry.