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Abstract Homeostasis of protein concentrations in cells is crucial for their proper functioning, requiring steady-state concentrations to be stable to fluctuations. Since gene expression is regulated by proteins such as transcription factors (TFs), the full set of proteins within the cell constitutes a large system of interacting components, which can become unstable. We explore factors affecting stability by coupling the dynamics of mRNAs and proteins in a growing cell. We find that mRNA degradation rate does not affect stability, contrary to previous claims. However, global structural features of the network can dramatically enhance stability. Importantly, a network resembling a bipartite graph with a lower fraction of interactions that target TFs has a higher chance of being stable. Scrambling the E. coli transcription network, we find that the biological network is significantly more stable than its randomized counterpart, suggesting that stability constraints may have shaped network structure during the course of evolution.
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The intracellular environment affects protein–protein interactions
Protein–protein interactions are essential for life but rarely thermodynamically quantified in living cells. In vitro efforts show that protein complex stability is modulated by high concentrations of cosolutes, including synthetic polymers, proteins, and cell lysates via a combination of hard-core repulsions and chemical interactions. We quantified the stability of a model protein complex, the A34F GB1 homodimer, in buffer, Escherichia coli cells and Xenopus laevis oocytes. The complex is more stable in cells than in buffer and more stable in oocytes than E. coli . Studies of several variants show that increasing the negative charge on the homodimer surface increases stability in cells. These data, taken together with the fact that oocytes are less crowded than E. coli cells, lead to the conclusion that chemical interactions are more important than hard-core repulsions under physiological conditions, a conclusion also gleaned from studies of protein stability in cells. Our studies have implications for understanding how promiscuous—and specific—interactions coherently evolve for a protein to properly function in the crowded cellular environment.
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- PAR ID:
- 10225392
- Date Published:
- Journal Name:
- Proceedings of the National Academy of Sciences
- Volume:
- 118
- Issue:
- 11
- ISSN:
- 0027-8424
- Page Range / eLocation ID:
- e2019918118
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1073/pnas.2019918118
