Protein turnover is vital to cellular homeostasis. Many proteins are degraded efficiently only after they have been post-translationally “tagged” with a polyubiquitin chain. Ubiquitylation is a form of Post-Translational Modification (PTM): addition of a ubiquitin to the chain is catalyzed by E3 ligases, and removal of ubiquitin is catalyzed by a De-UBiquitylating enzyme (DUB). Nearly four decades ago, Goldbeter and Koshland discovered that reversible PTM cycles function like on-off switches when the substrates are at saturating concentrations. Although this finding has had profound implications for the understanding of switch-like behavior in biochemical networks, the general behavior of PTM cycles subject to synthesis and degradation has not been studied. Using a mathematical modeling approach, we found that simply introducing protein turnover to a standard modification cycle has profound effects, including significantly reducing the switch-like nature of the response. Our findings suggest that many classic results on PTM cycles may not hold in vivo where protein turnover is ubiquitous. We also found that proteins sharing an E3 ligase can have closely related changes in their expression levels. These results imply that it may be difficult to interpret experimental results obtained from either overexpressing or knocking down protein levels, since changes in protein expression can be coupled via E3 ligase crosstalk. Understanding crosstalk and competition for E3 ligases will be key in ultimately developing a global picture of protein homeostasis.

蛋白质更新对于细胞稳态至关重要。许多蛋白质只有在翻译后用多聚泛素链“标记”后才能有效降解。泛素化是翻译后修饰（PTM）的一种形式：通过E3连接酶催化在链上添加泛素，而去泛素化酶（DUB）催化泛素的去除。大约四十年前，Goldbeter和Koshland发现，当底物处于饱和浓度时，可逆PTM循环的功能类似于通断开关。尽管此发现对生化网络中类似开关行为的理解具有深远的意义，但尚未研究受合成和降解作用的PTM循环的一般行为。使用数学建模方法，我们发现，简单地将蛋白质更新引入标准修饰周期会产生深远的影响，包括显着降低响应的开关状性质。我们的发现表明，关于PTM周期的许多经典结果可能不成立体内的蛋白质更新无处不在。我们还发现，共享E3连接酶的蛋白质在其表达水平上可能具有密切相关的变化。这些结果暗示可能难以解释从过表达或降低蛋白水平获得的实验结果，因为蛋白表达的变化可以通过E3连接酶串扰耦合。了解串扰和E3连接酶的竞争将是最终发展蛋白质稳态的全球图景的关键。