Protein binding and catalysis in crowded environments: from in vitro to in vivo (#16)
While most biological reactions occur within the complex environment of the cell, their investigation was primarily done in the test tube under dilute solution conditions. To bring binding studies closer to the in vivo environment, we investigated the role of crowding and the cellular environment on binding and catalysis. For crowding we added various polymers to the solution, including Dextran and PEGs of different molecular weights and cell extracts. While crowding enhances oligomerization and polymerization of macromolecules, it has only a small effect on the binding rates and affinities of transient protein-protein interactions. Next, we developed a method to follow binding in real time also in living cells. We found that the rates of association were close to those measured in the test tube in simple solutions, with variations between single cells and the magnitude of electrostatic forces acting between the interacting proteins. We suggest that the limited effect of crowders, which is much bellow the expected from the increased viscosity of the solutions, is a result of the occluded volume effect in high crowder concentrations. Direct measurements of the stability and structure of the encounter complex along the association pathway shows that crowders have only a minor effect on K1 or k2, and do not change the shape or size of the encounter complex. Following these studies, we initiated a program to investigate enzymatic reaction constants, Km and kcat in living cells. Initial results, and methods to analyze them will be presented in light of the occluded volume effect of crowders.
- Phillip, Y., Harel, M., Khait, R., Qin, S., Zhou, H. X. & Schreiber, G. (2012). Contrasting factors on the kinetic path to protein complex formation diminish the effects of crowding agents. Biophys J 103, 1011-1019.
- Phillip, Y., Kiss, V. & Schreiber, G. (2012). Protein-binding dynamics imaged in a living cell. Proc Natl Acad Sci U S A 109, 1461-1466.
- Phillip, Y. & Schreiber, G. (2013). Formation of protein complexes in crowded environments - From in vitro to in vivo. FEBS Lett 587, 1046-1052