Maximum entropy determination of mammalian proteome dynamics

• 成果类型: Article
• 署名作者: Dear, Alexander J.; Garcia, Gonzalo A.; Meisl, Georg; Collins, Galen A.; Knowles, Tuomas P. J.; Goldberg, Alfred L.
• 署名单位: Harvard University; Harvard Medical School; University of Cambridge; Mississippi State University; University of Cambridge
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-14921
• DOI: 10.1073/pnas.2313107121
• 发表日期: 2024-04-30
• 关键词: newly synthesized proteins; ubiquitin-proteasome; quality-control; cotranslational ubiquitination; abnormal proteins; 26s proteasomes; cells reveals; degradation; quantification; STABILITY

摘要

Full understanding of proteostasis and energy utilization in cells will require knowledge of the fraction of cell proteins being degraded with different half-lives and their rates of synthesis. We therefore developed a method to determine such information that combines mathematical analysis of protein degradation kinetics obtained in pulse-chase experiments with Bayesian data fitting using the maximum entropy principle. This approach will enable rapid analyses of whole-cell protein dynamics in different cell types, physiological states, and neurodegenerative disease. Using it, we obtained surprising insights about protein stabilities in cultured cells normally and upon activation of proteolysis by mTOR inhibition and increasing cAMP or cGMP. It revealed that >90% of protein content in dividing mammalian cell lines is long-lived, with half-lives of 24 to 200 h, and therefore comprises much of the proteins in daughter cells. The well-studied short-lived proteins (half-lives < 10 h) together comprise <2% of cell protein mass, but surprisingly account for 10 to 20% of measurable newly synthesized protein mass. Evolution thus appears to have minimized intracellular proteolysis except to rapidly eliminate misfolded and regulatory proteins.