What Macromolecular Crowding Can Do to a Protein

Abstract

The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area.

How High Concentrations of Proteins Stabilize the Amorphous State of Calcium Orthophosphate: A Solid-State Nuclear Magnetic Resonance (NMR) Study of the Casein Case

“…These consequences are the response of the protein to the need of minimizing excluded volumes in dense systems. 24 If such effects are important in the present system, the formation of more compact, proteincluster complexes would be favored since it would decrease the excluded volume. This effect should also counter any eventual increase in the number and/or the size of the clusters since such changes will necessarily increase the excluded volume.…”

“…Actually, 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59excluded volume effects could play a role in this increase. Previous works in dense, pure, protein systems show that the increase in concentration induces a strong increase in protein-protein interactions 24 with mainly two possible consequences: a change in protein conformation (adopting more compact conformation) and/or an increase in protein aggregation. These consequences are the response of the protein to the need of minimizing excluded volumes in dense systems.…”

Weak protein–protein interactions in live cells are quantified by cell-volume modulation

“…At such short times, regulatory actions taken by the cell to cope with the change in volume, such as synthesizing channels, chaperones, and enzymes are scarcely initiated (24,25). Thus, fast volume change affects viscosity (26), crowding (27,28), protein structure (29,30), activity (31), and quinary interactions within the cell purely by physico-chemical means. Cell volume can be controlled by changing medium osmotic pressure-another parameter that varies in biological settings: Extracellular osmolarity fluctuates routinely for some mammalian cells, including kidney (32), cartilage (33), and even in the blood under certain pathological conditions (34).…”

Dissociative mechanism for irreversible thermal denaturation of oligomeric proteins

“…Macromolecular crowding exerts influence on the equilibrium and kinetics of macromolecular reactions in which there exists a significant difference between the volume excluded to reactants and the volume excluded to products (Minton 2001). Such reactions include protein isomerization, folding/unfolding and prot e i n -p r o t e i n i n t e r a c t i o n s ( C h e b o t a r e v a 2 0 0 7 ; Chebotareva et al 2001Chebotareva et al , 2004Chebotareva et al , 2010Chebotareva et al , 2013Chebotareva et al , 2015aEllis 2001;Ellis and Minton 2003;Gruebele et al 2016;Hall and Minton 2003;Kurganov and Chebotareva 2013;Kuznetsova et al 2014;Minton 2001;Roman et al 2011Roman et al , 2016Sluchanko et al 2015;Wills and Winzor 2011;Zhou et al 2008). Macromolecules (proteins, polysaccharides, neutral polymers) as well as low-molecular-weight compounds (for example, osmolytes) can be used in model experiments as crowding agents (Chebotareva et al 2001(Chebotareva et al , 2004Davis-Searles et al 2001;Ellis 2001;Jiao et al 2010;Roman et al 2011;Sluchanko et al 2015).…”