Macromolecular Crowding and Intrinsically Disordered Proteins: A Polymer Physics Perspective

Abstract

The cell is a crowded environment where a relevant fraction of the available space is occupied by proteins, nucleic acids, and metabolites. Here we discuss recent advancements in the understanding of crowding effects on intrinsically disordered proteins. Differently from their structured counterparts, these proteins do not adopt a stable three-dimensional structure and remain flexible and dynamic in solution. The physics of polymers and colloids provides a framework to interpret how crowding modulates conformations, dynamics, and interactions of disordered proteins. Flory-Huggins models enable rationalizing the different degree of compaction induced by crowding agents in terms of depletion interactions. The same interactions modulate the diffusion of the disordered proteins in a crowded milieu and the association and dissociation rates when interacting with a ligand. Altogether, this theoretical framework provides new insights into the interpretation of the effects of the cellular environment on disordered proteins.

Structure and Transition Dynamics of Intrinsically Disordered Proteins Probed by Single-Molecule Spectroscopy

“…The ratio between charge and hydropathy (commonly referred to as, C/H) of IDPs regulates the extent of compactness. , Using different IDPs having varied amino acid sequences, Choi et al. characterized their molecular dimensions from smFRET measurements .…”

“…18 Thus, molecular crowders in the structural transitions of IDPs serve as reasonable mimicking agents under in vitro conditions, thereby enabling us to draw a scientific analogy with the conditions encountered in the in vivo environments. 18,19 Schuler and co-workers quantified the role of crowding induced by common polymers. 10 They demonstrated that a reduction in the structure of IDPs occurs upon increasing the concentration and the size of the crowder.…”

“…The ratio between charge and hydropathy (commonly referred to as, C/H) of IDPs regulates the extent of compactness. 19,23 Using different IDPs having varied amino acid sequences, Choi et al characterized their molecular dimensions from smFRET measurements. 24 The nature of conformational flexibility of five different synaptic IDPs has been outlined using singlemolecule characterizations with the help of a polymer model.…”

“…To overcome this, research based on the dynamics of biomolecules in the presence of molecular crowders has garnered sufficient interest of late . Thus, molecular crowders in the structural transitions of IDPs serve as reasonable mimicking agents under in vitro conditions, thereby enabling us to draw a scientific analogy with the conditions encountered in the in vivo environments. , …”

The biophysics of disordered proteins from the point of view of single-molecule fluorescence spectroscopy

“…The large spectrum of scaling exponents observed under native conditions for different unfolded and disordered proteins [53,64,70,71] reflects the contribution of sequence composition on the conformations of disordered ensembles. Müller-Späth et al [72] used single-molecule FRET to probe the conformations of unfolded proteins, showing the degree of compaction and expansion of the interdye distance depends on the charged residue content in the protein, and acceptor-acceptor (AA) exhibits a correlated decay, whereas the cross-correlation (AD) shows an anticorrelated increase in the signal.…”