Molecular crowding

  Stokes-Einstein Relation Copyright: © Fitter The size relation between the diffusing tracer molecule and the crowder molecule is crucial for the translational diffusion of biological tracer molecules.

Most of our general knowledge about biological chemistry or biochemistry stems from experiments on dilute samples of macromolecules, like proteins, or DNA, at concentrations of about a few grams per liter. However, these conditions are surprisingly different from those inside living cells. The cellular cytoplasm is crowded with many different macromolecules reaching concentrations with hundreds of grams per liter. Hence, a substantial fraction (up to 20%) of the total volume of any cell is occupied by macromolecules. This so-called excluded volume increases the effective concentration of molecules and affects the physical properties of the solution (“excluded volume” effect). For example, the molecular mobility and dynamics within constrained volumes are suppressed in the cytosol, characterized by a high concentration of large and small molecules. As a consequence, molecular crowding decreases the diffusion rate, shifts the equilibrium of protein-protein association and of protein-substrate interactions and changes the conformational dynamics of proteins. We performed FCS studies on several biological macromolecules, like proteins, protein-complexes or ribosomes, which are dissolved in highly concentrated polymer solutions. For this purpose we make use of synthetic polymers (PEG, Ficoll) of different molecular weights ranging from 5-400 kDa, which mimic the cellular crowding.


Related publications

Skóra T, Vaghefikia F, Fitter J, and Kondrat S.
Macromolecular Crowding: How Shape and Interactions Affect Diffusion
J. Phys. Chem. B 2020, 124,7537-7543.

Niklas O. Junker, Farzaneh Vaghefikia, Alyazan Albarghash, Henning Höfig, Daryan Kempe, Julia Walter, Julia Otten, Martina Pohl, Alexandros Katranidis, Simone Wiegand, and Jörg Fitter
Impact of Molecular Crowding on Translational Mobility and Conformational Properties of Biological Macromolecules
J Phys Chem B. 123, 4477-4486 (2019)