Probing Electrostatic and Hydrophobic Associative Interactions in Cells

Weak nonspecific interactions between biomacromolecules determine the cytoplasmic organization. Despite their importance, it is challenging to determine these interactions in the intracellular dense and heterogeneous mixture of biomacromolecules. Here, we develop a method to indicate electrostatic and hydrophobic associative interactions and map these interactions. The method relies on a genetically encoded probe containing a sensing peptide and a circularly permuted green fluorescent protein that provides a ratiometric readout. Inside bacterial and mammalian cells, we see that the cytoplasmic components interact strongly with cationic and hydrophobic probes but not with neutral hydrophilic probes, which remain inert. The Escherichia coli cytoplasm interacts strongly with highly negatively charged hydrophilic probes, but the HEK293T cytoplasm does not. These associative interactions are modulated by ATP depletion. Hence, the nonspecific associative interaction profile in cells is condition- and species-dependent.