NMR Study of Polymer Diffusion in the Presence of a Biological Intracellular Crowder

Abstract

Protein interactions take place in the crowded and heterogeneous intracellular milieu with macromolecular concentrations up to 400 mg/ml. The role of excluded-volume effects and soft non-specific interactions in macromolecular crowding has been traditionally studied in artificial crowders like Ficoll and dextran. Our measurements of flow properties show, however, that artificial crowders such as Ficoll have starkly different rheological characteristics from a complex biological crowder, bacterial cell lysate, at comparable concentrations. Moreover, biological crowders are a heterogeneous collection of biomolecules with a distribution of sizes, shapes and charge; these differences likely also affect translational diffusion of biomolecules within the cell. In this study, we examine the effects of size distribution and charge of a complex biological crowder on the diffusion of polymers and ask if this is similar to what is seen for artificial crowders like Ficoll. To answer this question, we use a top-down experiment using bacterial cell lysate as the crowder. To test the dynamical properties of polymer in the lysate environment, we measure the translational diffusion of the test polymer polyethylene glycol (PEG) using diffusion NMR. While PEG is not a biomolecule, it is a useful analog for a disordered protein. Our rheological tests show that while Ficoll is nearly Newtonian even at high concentrations, bacterial cell lysate is markedly viscoelastic. Results will provide a better understanding of the effects of complex biological crowders on polymer diffusion.