Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae

[abridged] Background: The distribution of chemical species in an open system at metastable equilibrium can be expressed as a function of environmental variables which can include temperature, oxidation-reduction potential and others. Calculations of metastable equilibrium for various model systems were used to characterize chemical transformations among proteins and groups of proteins found in different compartments of yeast cells. Results: With increasing oxygen fugacity, the relative metastability fields of model proteins for major subcellular compartments go as mitochondrion, endoplasmic reticulum, cytoplasm, nucleus. In a metastable equilibrium setting at relatively high oxygen fugacity, proteins making up actin are predominant, but those constituting the microtubule occur with a low chemical activity. A reaction sequence involving the microtubule and spindle pole proteins was predicted by combining the known intercompartmental interactions with a hypothetical program of oxygen fugacity changes in the local environment. In further calculations, the most-abundant proteins within compartments generally occur in relative abundances that only weakly correspond to a metastable equilibrium distribution. However, physiological populations of proteins that form complexes often show an overall positive or negative correlation with the relative abundances of proteins in metastable assemblages. Conclusions: This study explored the outlines of a thermodynamic description of chemical transformations among interacting proteins in yeast cells. The results suggest that these methods can be used to measure the degree of departure of a natural biochemical process or population from a local minimum in Gibbs energy.

💡 Research Summary

The paper presents a thermodynamic framework for evaluating the relative metastabilities of proteins localized in different subcellular compartments of the yeast Saccharomyces cerevisiae. Starting from the premise that an open biochemical system can attain a metastable equilibrium—where the distribution of chemical species is governed by the minimization of Gibbs free energy under given environmental constraints—the authors construct a quantitative model that incorporates temperature, pH, and, most importantly, the oxygen fugacity (ƒO₂) as variables.

To operationalize the model, representative “model proteins” are selected for each major compartment (mitochondrion, endoplasmic reticulum, cytoplasm, nucleus). For each protein the elemental composition (C, H, N, O, S) and a standard Gibbs free energy of formation (ΔG⁰) are calculated from published amino‑acid thermodynamic data. These values are then combined into a global Gibbs energy function for the whole cell, allowing the computation of the composition that minimizes the free energy at any specified set of environmental parameters. By systematically varying ƒO₂ while holding temperature and pH constant, the authors map out “metastability fields” for each compartment.

The calculations reveal a clear ordering of compartments with increasing oxygen fugacity: mitochondrion → endoplasmic reticulum → cytoplasm → nucleus. In low‑ƒO₂ conditions the mitochondrial protein assemblage is thermodynamically favored, whereas at high ƒO₂ the nuclear proteins become the most stable. A striking result is that actin‑related proteins dominate the metastable assemblage under high‑oxygen conditions, while tubulin (the building block of microtubules) and spindle‑pole proteins exhibit very low chemical activities, effectively being excluded from the metastable set. This suggests that the oxidative environment can shift the balance between cytoskeletal elements, potentially influencing cell shape and division.

The authors then compare the metastable predictions with empirical proteomic data. The most abundant proteins in each compartment show only a weak positive correlation with the calculated metastable abundances, indicating that cells do not simply occupy the global free‑energy minimum. However, proteins that form stable complexes tend to display either a modest positive or negative correlation, hinting that functional constraints and protein‑protein interactions modulate the degree to which the system approaches metastable equilibrium.

To illustrate the dynamic aspect of the model, the authors integrate known inter‑compartmental interaction networks (e.g., microtubule–spindle pole relationships) with a hypothetical temporal program of changing ƒO₂. By simulating a stepwise increase or decrease in oxygen fugacity, they predict a sequence of reactions: microtubule components become destabilized, spindle‑pole proteins are recruited, and eventually actin‑based structures become predominant. This exercise demonstrates how environmental redox shifts could drive coordinated re‑organization of the cytoskeleton and related organelles.

Finally, the concept of “departure from a local Gibbs minimum” is introduced as a quantitative metric for assessing how far a real biochemical population deviates from its metastable equilibrium. By calculating the Euclidean distance between observed protein abundances and the metastable distribution, the authors provide a tool for measuring the non‑equilibrium character of cellular states, such as stress responses, metabolic reprogramming, or disease‑associated dysregulation.

In summary, the study establishes a thermodynamic description of protein distribution across subcellular compartments, demonstrates that oxygen fugacity is a key determinant of relative protein metastability, and shows that while the cell’s proteome does not fully align with the metastable minimum, the degree of alignment correlates with functional protein complexes. The methodology offers a novel bridge between physical chemistry and systems biology, opening avenues for quantitative analyses of non‑equilibrium processes in living cells and for the design of engineered metabolic or structural pathways that exploit redox‑driven metastability.