Intrinsically disordered proteins in crowded milieu: when chaos prevails within the cellular gumbo

Abstract

Effects of macromolecular crowding on structural and functional properties of ordered proteins, their folding, interactability, and aggregation are well documented. Much less is known about how macromolecular crowding might affect structural and functional behaviour of intrinsically disordered proteins (IDPs) or intrinsically disordered protein regions (IDPRs). To fill this gap, this review represents a systematic analysis of the available literature data on the behaviour of IDPs/IDPRs in crowded environment. Although it was hypothesized that, due to the excluded-volume effects present in crowded environments, IDPs/IDPRs would invariantly fold in the presence of high concentrations of crowding agents or in the crowded cellular environment, accumulated data indicate that, based on their response to the presence of crowders, IDPs/IDPRs can be grouped into three major categories, foldable, non-foldable, and unfoldable. This is because natural cellular environment is not simply characterized by the presence of high concentration of "inert" macromolecules, but represents an active milieu, components of which are engaged in direct physical interactions and soft interactions with target proteins. Some of these interactions with cellular components can cause (local) unfolding of query proteins. In other words, since crowding can cause both folding and unfolding of an IDP or its regions, the outputs of the placing of a query protein to the crowded environment would depend on the balance between these two processes. As a result, and because of the spatio-temporal heterogeneity in structural organization of IDPs, macromolecular crowding can differently affect structures of different IDPs. Recent studies indicate that some IDPs are able to undergo liquid-liquid-phase transitions leading to the formation of various proteinaceous membrane-less organelles (PMLOs). Although interiors of such PMLOs are self-crowded, being characterized by locally increased concentrations of phase-separating IDPs, these IDPs are minimally foldable or even non-foldable at all (at least within the physiologically safe time-frame of normal PMLO existence).

Prion protein PrP nucleic acid binding and mobilization implicates retroelements as the replicative component of transmissible spongiform encephalopathy

“…RNA binding by IDRs is crucially important for liquid-liquid phase separation [123], attributed to high local concentrations of negative charges [124]. The IDR not only extends the ligand-capture radius of the protein but also permits refolding of the IDR into an ordered 3D structure in response to ligand binding [125,126]. Droplets are composed of diverse RNA-binding proteins in association with different RNA species, notably non-coding RNA, undergo liquid-liquid phase transitions, and dynamically assemble and disassemble, and components can exchange with the surrounding liquid phase within seconds to minutes [124].…”

Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding

“…Macromolecular crowding can affect protein–target binding and protein folding . In particular, the malleability of IDPs/IDRs makes them susceptible to the influence of macromolecular crowders . Conformational compaction of IDPs/IDRs by macromolecular crowders has been observed, where the effect depends not only on the crowder size and concentration, but also on the properties of IDPs/IDRs .…”

“…155 In particular, the malleability of IDPs/IDRs makes them susceptible to the influence of macromolecular crowders. 156,157 Conformational compaction of IDPs/ IDRs by macromolecular crowders has been observed, where the effect depends not only on the crowder size and concentration, but also on the properties of IDPs/IDRs. [158][159][160][161][162][163] MAP2c, p21 Cip1 , and FlgM show global compaction and local structuring in crowded conditions.…”

Bridging protein structure, dynamics, and function using hydrogen/deuterium‐exchange mass spectrometry

“…IDPs are critical for a number of diverse cellular processes and individual IDPs are often functionally promiscuous. The large range of IDP functionalities are likely derived from their inherent conformational plasticity . IDPs are challenging to study using HDX‐MS for a number of reasons; significant flexibility and a lack of secondary structure means IDPs require very short, rapid deuteration time points under physiological conditions.…”