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Ribosomes are the factories in cells that synthesize proteins. When cells grow faster, there are not enough ribosomes to keep up with the demand for faster protein synthesis without individual ribosomes becoming more productive.

No abstract

Research on protein-protein interaction (PPIs) tends to focus on high affinity interactions. Weaker interactions (Kd > 1 µM) recently understood as contributing to intracellular phase separation suggest that even-weaker PPIs might also matter in as-yet unknown ways. However, ultra-weak PPIs (Kd > 1 mM) are not readily accessible by in vivo techniques. Here we use protein electrostatics to estimate PPI strengths and spatially-resolved dynamic simulations to investigate the potential impacts of ultra-weak PPIs within dense protein suspensions. We find that ultra-weak PPIs can drive formation of transient clusters that last long enough to enable enzyme-catalyzed reactions and accelerate the sampling of protein associations. We apply our method to Mycoplasma genitalium , finding that ultra-weak PPIs should be ubiquitous among cytoplasmic proteins. We also predict that the proteome-wide interactome can be shifted to favor 'binding-dominant' ultra-weak PPIs via the introduction of a few charged protein complexes. We speculate that ultra-weak PPIs could contribute to cellular fitness by facilitating sampling and colloidal-scale transport of proteins involved in biological processes, including protein synthesis.

SummaryFaster growing cells must make proteins more quickly. This occurs in part through increasing total ribosome abundance. However, the productivity of individual ribosomes also increases, almost doubling via an unknown mechanism. To investigate, we model both physical transport and chemical reactions among ensembles of individual molecules involved in translation elongation in Escherichia coli. We predict that the Damköhler number, the ratio of transport latency to reaction latency, for translation elongation is ~4; physical transport of individual ternary complexes accounts for ~80% of elongation latency. We also model how molecules pack closer together as growth quickens. Although denser cytoplasm both decreases transport distances and hinders motion, we predict that decreasing distance wins out, offering a simple mechanism for how individual elongating ribosomes become more productive as growth quickens. We also quantify how crowding imposes a physical limit on the performance of self-mixing molecular systems and likely undergirds cellular behavior more broadly.