Perspective: a stirring role for metabolism in cells

Abstract

Based on recent findings indicating that metabolism might be governed by a limit on the rate at which cells can dissipate Gibbs energy, in this Perspective, we propose a new mechanism of how metabolic activity could globally regulate biomolecular processes in a cell. Specifically, we postulate that Gibbs energy released in metabolic reactions is used to perform work, allowing enzymes to self-propel or to break free from supramolecular structures. This catalysis-induced enzyme movement will result in increased intracellular motion, which in turn can compromise biomolecular functions. Once the increased intracellular motion has a detrimental effect on regulatory mechanisms, this will establish a feedback mechanism on metabolic activity, and result in the observed thermodynamic limit. While this proposed explanation for the identified upper rate limit on cellular Gibbs energy dissipation rate awaits experimental validation, it offers an intriguing perspective of how metabolic activity can globally affect biomolecular functions and will hopefully spark new research.

Keywords: Gibbs energy; active matter; enhanced diffusion; metabolism; regulation.

Figure 1. Cellular Gibbs energy dissipation rate has an upper limit and may be explained by metabolism‐induced molecular motion

(A) A cell encompasses a large number of interconnected chemical reactions, forming a metabolic network (left panel); each reaction is catalyzed by an enzyme and is characterized by two parameters: its Gibbs energy of reaction, ΔG, and its flux, v (middle panel). The product of the Gibbs energy of reaction and the flux is the Gibbs energy dissipation rate. When this parameter is summed across all the reactions in the metabolic network, the cellular Gibbs energy dissipation rate is obtained. The cellular Gibbs energy dissipation rate has units of J/h, or J/gDW/h if normalized to the cell dry biomass. We previously found that this parameter reaches an upper limit, at moderately high growth rates/substrate uptake rates (Niebel et al, 2019) (right panel). Constrained by this upper limit, cells that have reached the “plateau” may still achieve increased growth rates provided that metabolic fluxes are redirected towards reactions that dissipate less Gibbs energy. The interplay between the upper limit and metabolism is represented by the negative feedback arrow. (B) To explain the existence of this limit, we propose that catalysis leads to enhanced enzyme motion (left panel). In the crowded intracellular environment (middle panel), excessive motion will ultimately cause detrimental effects on biomolecular functions (right panel).

Figure 2. Increased molecular motion can occur at hardly increased temperature

(A) According to the equipartition theorem, the average energy of all degrees of freedom (rotation, vibration, and translation) is the same, and equal to $\frac{1}{2}{k}_{B}T$. Under these conditions, the diffusion coefficient can be estimated from the Stokes–Einstein equation, and the enzyme is said to undergo thermal Brownian motion (see definition in Table 1). (B) For an enzyme driven out of equilibrium by the Gibbs energy released during catalysis, the equal distribution of energy among the various degrees of freedom no longer applies, and the diffusion coefficient may not abide by the Stokes–Einstein equation, potentially being larger than the value predicted by this equation. (C) As it moves, the enzyme also dissipates energy to its surroundings as heat, which is swiftly transferred to the environment. (D) The loss of energy brings the enzyme back to its initial equilibrium state with the local surroundings.

Figure 3. Mechanisms for enzyme self‐propulsion by work performed

(A) Phoretic effects, in which an enzyme moves without necessarily having to change its conformation. This motion may be accomplished when local gradients around the enzyme are established during catalysis. These gradients can be of different nature: temperature, ΔT (self‐thermophoresis (Golestanian, 2015), left panel); electrostatic potential, ∆V (self‐electrophoresis (Muddana et al, 2010), middle panel), as a result of a differential accumulation of positive (+) and negative (−) charges; or substrate (A) or product (B) concentration, ∆C (self‐diffusiophoresis (Golestanian et al, ; Banigan & Marko, 2016), right panel). (B) Conformational changes, leading to active swimming motion, either by asymmetric pressure waves across the enzyme (chemoacoustic effect (Riedel et al, 2015), top panel), or by directional movement of its structural elements around a fixed point or axis (Slochower & Gilson, 2018) (bottom panel).

Figure 4. Work performed by an enzyme can lead to its breaking free from a supramolecular structure

(A) Due to the high concentration of macromolecules in the cell, proteins can establish multivalent interactions with each other and with other molecules. These interactions can arise between charged (electrostatic interactions, dotted lines), or uncharged parts of each molecule (dashed lines); hydrogen bonds may also be established (parallel dashed lines). (B) Such interactions can be counteracted by the release of Gibbs energy in enzymatic reactions, which allow the enzymes to momentarily escape the supramolecular structure and undergo unhindered diffusive motion. (C) When the energy is dissipated to its surroundings, the protein re‐attaches to the supramolecular structure.

Figure 5. Proposed explanation for the mechanistic basis of the observed limit on the cellular Gibbs energy dissipation rate

(A) In metabolically active cells, enzyme catalysis leads to the release of Gibbs energy and results in an increase in enzyme motion. (B) Since the intracellular environment (and cytoplasm, in particular) is highly crowded, collisions between enzymes and other molecules will take place. (C) This increase in motion and collisions impacts various biomolecular functions, for example, transcription. (D) Increased motion can be detrimental for protein folding. (E) Phase separation may be affected by increased molecular motion. Together with other effects, this may ultimately regulate the cell’s metabolic activity, as depicted by the gray negative feedback arrow. The regulation of metabolic activity is expected to control the Gibbs energy dissipation rate, g^diss , and maintain it below its upper limit (Niebel et al, 2019).