Transient diffusive protein-protein interactions in live cells - functional optimisation on meso- and microscopic levels.

A striking feature of nucleic acids and lipid membranes is that they all carry net-negative charge, and so is true for the majority of intracellular proteins. It is suggested that the role of this negative charge is to assure a basal inter-molecular repulsion that keeps the cytosolic content suitably ‘fluid’ for function. Unlike the situation in test tubes, any functional protein-protein interaction in the cytosol is subject to competition from the densely crowded background, i.e. surrounding stickiness. At the nonspecific limit of this stickiness is the ‘random’ protein-protein association, maintaining profuse populations of transient and constantly interconverting complexes at physiological protein concentrations. The phenomenon is readily quantified in studies of the protein rotational diffusion, showing that the more net negatively charged a protein is the less it is retarded by clustering. In-cell NMR can be used to study how specific protein properties modulate this cross-talk with the cytosolic environment, and conversely: How constant collisions and formation of ransom transient encounter complexes are affecting basal protein properties. Random encounters between proteins in crowded cells are by no means passive, but found to be under selective control, which e.g., enables proteome solubility, optimise the diffusive search for interaction partners, and allow for an adaptation to environmental extremes. Interestingly, the residues that modulate the random encounters act mainly mesoscopically through protein net charge, meaning that their detailed signatures vary across organisms with different intracellular constraints. To further examine such variations, we compare the diffusive behaviour of one bacterial and two human proteins in the E. coli and the human cytosols, using in-cell NMR relaxation. We find that proteins that ‘stick’ and whose signals become broadened beyond detection in E. coli are generally less restricted in mammalian cells. This dynamic protein-protein interplay is under evolutionary control and
finely tuned across organisms to maintain optimal physicochemical conditions for the cellular processes. The emerging picture is then that specific cellular function relies on close competition between numerous weak and strong interactions, and where all parts of the protein surfaces are involved. The outstanding challenge
is now to decipher the very basics of this many-body system: how the detailed patterns of charged, polar and hydrophobic side chains not only control protein-protein interactions at close- and long- range, but also the collective properties of the cellular interior as a whole.