Relevance of Electrostatic Charges in Compactness, Aggregation, and Phase Separation of Intrinsically Disordered Proteins

Abstract

The abundance of intrinsic disorder in the protein realm and its role in a variety of physiological and pathological cellular events have strengthened the interest of the scientific community in understanding the structural and dynamical properties of intrinsically disordered proteins (IDPs) and regions (IDRs). Attempts at rationalizing the general principles underlying both conformational properties and transitions of IDPs/IDRs must consider the abundance of charged residues (Asp, Glu, Lys, and Arg) that typifies these proteins, rendering them assimilable to polyampholytes or polyelectrolytes. Their conformation strongly depends on both the charge density and distribution along the sequence (i.e., charge decoration) as highlighted by recent experimental and theoretical studies that have introduced novel descriptors. Published experimental data are revisited herein in the frame of this formalism, in a new and possibly unitary perspective. The physicochemical properties most directly affected by charge density and distribution are compaction and solubility, which can be described in a relatively simplified way by tools of polymer physics. Dissecting factors controlling such properties could contribute to better understanding complex biological phenomena, such as fibrillation and phase separation. Furthermore, this knowledge is expected to have enormous practical implications for the design, synthesis, and exploitation of bio-derived materials and the control of natural biological processes.

1. Introduction

Intrinsically disordered proteins (IDPs) and protein regions (IDRs) escape the paradigm of protein folding and must, rather, be described as conformational ensembles of interconverting conformers. Conformers of biological relevance can be poorly populated and cannot be easily isolated, unless bound to a ligand or partner acting as a conformational stabilizer [1]. The cellular environment (pH, temperature, ionic force, concentration of osmolytes) can influence the relative distribution of such metastable conformers, thereby acting as biochemical sensors and signal transducers [2]. Not surprisingly, IDRs are often located at the protein N- or C-terminus and act as interaction hubs in protein–protein networks [3,4]. This feature is instrumental to IDP/IDR involvement in crucial physiological processes, such as transcription, translation, and cell cycle regulation [2,5,6,7], and underlies the relationships between IDPs/IDRs and diseases (cancer, inflammation, or neurodegeneration) [8,9]. A central challenge for structural biology is understanding how sequence and sequence composition encode structural disorder. Depletion in hydrophobic residues, enrichment in structure-breakers (particularly prolines and glycines), along with polar and charged residues, represent the most common compositional traits and have been employed as diagnostic traits of structural disorder [10,11].

In IDPs/IDRs, the most frequent amino acids with ionizable side chains (i.e., groups that ionize between pH 1 and 14) are Asp and Glu, Lys, and Arg. The ionization behavior is mainly dictated by their equilibrium constant of acid dissociation (the “intrinsic pK_a” value) and their electrostatic environment, including pH. Under physiological conditions of nearly neutral pH, all these residues are charged, although their pK_a can be influenced by several factors, such as dehydration by the Born effect, Coulomb and charge–dipole interactions [12]. Hence, the apparent pK_a can reflect the presence of neighboring peptide bonds, the proximity with other charged groups, hydrogen donors/acceptors, solvent exposition, or burial inside a protein structure, being very sensitive to local conformation [12,13]. Several experimental and computational techniques can be applied to obtain pK_a values of residues embedded in a protein structure. Among these, nuclear magnetic resonance (NMR) spectroscopy allows measurement of the pH dependence of chemical shifts. Such experiments have highlighted that Asp, Glu, and Lys residues in disordered polypeptides, as well as in solvent-exposed regions of ordered proteins [12], have pK_a values close to those measured in random coil models [14], with short- and medium-range interactions prevailing on long-range electrostatic ones [15,16]. Arg represents a peculiar case. On one side, it is highly basic due to charge delocalization; on the other side, the guanidinium group is a very weakly hydrated cation [17]. This latter property facilitates Arg residue burial in hydrophobic micro-environments [18] and its stacking interactions with aromatic protein residues [17,19]. Theoretical studies have modeled IDPs as ideal “charge-decorated” polymers, drawing copiously from polymer physics to describe their peculiar behavior [20,21,22,23,24]. Indeed, in polymer physics, IDPs have been referred to as either polyelectrolytes, with multiple charges of the same sign, or, more frequently (~75% of IDPs), as polyampholytes, carrying both positive and negative charges [25]. The (un)balancing of opposite charges, i.e., the extent of net charge, affects the IDP conformational fate: Electrical neutrality enables polyampholytes to collapse, whereas unbalanced charges result in structural expansion due to repulsive forces [26]. This review focuses on the parameters introduced so far to capture the peculiar electrostatics of IDPs/IDRs and the involvement of electrostatic properties in their physio-pathological roles. In particular, we will discuss how charge density and distribution affect IDP/IDR compactness, aggregation, solubility, fibrillation, and phase separation. Basic information on compaction parameters, fibrillation, and phase separation are presented in three appendices. Describing the mathematical formalisms underlying polypeptide structure goes beyond the aims of this review, which is meant to provide an overview of its practical implications of IDP conformational behavior in the field of protein science and cellular biochemistry.

2. From Mean Net Charge to Linear Patterns of Charged Residues

2.1. Compositional Classes of IDPs and Phase Diagrams of Protein Conformation

Protein collapsibility is governed by the interplay of intra-chain and chain–solvent interactions. The early concept of an empirical charge-hydropathy (C-H) correlation has been expressed by the so-called Uversky’s plot [27], which classifies IDPs/IDRs according to their position in the two-dimensional space of mean hydrophobicity “H” and mean net absolute charge “q”. This latter is equivalent to the absolute value of net charge per residue (|NCPR|), a more recently introduced parameter defined as the difference between the fractions of positively (f₊) and negatively (f₋) charged residues. In the original Uversky’s plot, the line “<q> = 2.785 <H> −1.151” demarcates the boundary between IDPs/IDRs and natively folded proteins [27], assigning the same coordinates to oppositely charged polymers. To account for the polarity of charged proteins, more recent versions of the C-H plot represent the full range of NCPR values (i.e., not only |NCPR|) with the “H-q” space crossed by two “mirror” boundaries (“<q> = 2.785 <H> −1.151” and “<q> = −2.785 <H> +1.151”) (Figure 1a) [28]. Still, such plots fail to capture differences that may underlie polymers with similar NCPR values yet endowed with a different number of charged residues. This issue has been illustrated by atomistic simulations and experimental investigations by Pappu’s group on a repertoire of protamines, small arginine-rich nuclear proteins [29]. In spite of their identical NCPR values, these polypeptides possess different dimensions and local conformational preferences. Therefore, with the aim of enhancing Uversky’s C-H phase diagram, the Mao-Pappu’s three-dimensional plot represents the hydrophobicity H on the vertical axis and (f₊) and (f₋) on two horizontal axes, where they vary independently and not cumulatively, as in the case of NCPR (Figure 1b) [29]. Thereby, sequences with low mean hydrophobicity, which initially were collectively considered as “natively unfolded proteins”, are now distinguished into “swollen coils” and “disordered globules”, according to their fractions of charged residues. When f₊ ≫ f₋ and vice versa, which implies large NCPR values, polypeptides can be considered as “polyelectrolytes” and may behave as extended swollen coils. Indeed, the presence of multiple unshielded charges induces chain expansion due to electrostatic repulsions and favorable polymer–solvent interactions, similarly to an ideal polymer in a good solvent [30,31]. On the other hand, when f₊ ≈ f₋, NCPR is close to zero, and polypeptides are “polyampholytes”, which behave as disordered globules governed by attractive interactions. Further, polyampholytes can be classified as “strong” or “weak”, depending on whether they possess a large or small fraction of charged residues (FCR, calculated as the sum of f₊ and f₋) and display specific conformational preferences.

An even better correlation between FCR and IDP conformations is offered by a more recent version of the conformational disorder plot, the so-called Das-Pappu’s phase diagram [11,25,32] (Figure 1c). Herein, low-NCPR IDPs/IDRs are no longer indiscriminately identified as globules, yet they occupy distinct conformational classes—globules, coils, hairpins, chimeras—according to their FCR values.

Table 1. Examples of intrinsically disordered proteins (IDPs) and protein regions (IDRs) belonging to the distinct regions of the Das-Pappu’s conformational phase diagram.

Protein Class	FCR	NCPR	Representative Proteins	References
R1, Globules	<0.25	<0.25	α-Synuclein (residues 1–100)	[11]
R2, Globules and coils	0.25 ≤ FCR ≤ 0.35	≤0.35	Tau repeat domain	[11]
R3, Polyampholyte coils or hairpins	>0.35	≤0.35	LEA_4 proteins 1, NSP1 2	[38]
R4, Polyelectrolytic semi-flexible rods or coils	>0.35	>0.35	Synthetic polyE and polyK; protamines, NP1 3; RAG2 4	[29,32]

¹ Late Embryogenesis Abundant proteins from Arabidopsis thaliana; ² nucleoporin Nsp1 (UniProt ID: P14907) of S. cerevisiae; ³ NP1 (UniProt ID: O13030), residues 5–24 of Cynops pyrrhogaster protamine 1; ⁴ RAG2 (UniProt ID: P21784), residues 392–411 (‘acidic hinge’) of Cricetulus griseus V(D)J recombination-activating protein 2.

lists some examples of proteins belonging to each of these conformational classes. Nevertheless, this classification, as clearly stated by the authors, is valid for IDPs/IDRs of at least 30 residues, with a low overall hydropathy and low proline content [25,32]. Furthermore, it does not provide any insight into how protein dimension varies within these classes [33]. When comparing experimental data with predictions inspired to FCR, or more complex composition-based heuristics, collapsed globules turn out to be less frequent than predicted [33,34,35,36]. Possible reasons for these discrepancies could be searched in the weaknesses of either the experimental or the computational approaches: (i) Collapsed globules have higher aggregation propensity compared to expanded coils, hampering structural characterization at the high protein concentrations required for some biophysical techniques (e.g., NMR, small-angle X-ray scattering (SAXS), etc.); and (ii) the efficiency of prediction algorithms could be hindered by the complexity of the intramolecular interactions’ governing compactness, as well as the interplay with the physicochemical environment [37].

2.2. The Concept of Linear Patterning of Charges and Its Parametrization

Asymmetry in electrostatic potentials is a recurrent feature in protein structure, found at the level of the protein backbone [39], secondary-structure elements [40], and supersecondary structure motifs [41]. Herein, we will focus on the effect of the charge distribution and polarization within the protein sequence, considering both the backbone structure and sequence-specific features encoded by the R-groups, i.e., its sequence specificity [37]. In this regard, an important aspect to be considered is the linear charge patterning. Indeed, while theoretical and computational works suggest that weak polyampholytes (i.e., low-FCR proteins) preferentially form globules, strong polyampholytes (i.e., high-FCR proteins) behave very differently from one another, according to the linear distribution of oppositely charged residues in their amino acid sequence [25].

The conformation of high-FCR proteins with an identical charge composition but different segregation of cationic and anionic residues was studied by Srivastava and Muthukumar already in the second half of the 1990s [26]. Monte Carlo (MC) simulations showed substantial differences in the radius of gyration (R_g, defined in Appendix A) between two groups of polymers, in which opposite charges are regularly interspersed or clustered at the two extremities, as a result of the interplay between intrachain electrostatic attractions and repulsions [26]. More recently, the same issue was systematically tackled by either computational simulations or scalable analytical theories, offering a coherent envision, yet using different parameters to quantitatively describe charge patterning. The group of Rohit Pappu has introduced the empirical parameter κ as a measure of the overall charge asymmetry [25]. Upon partitioning the protein sequence into N overlapping segments (or blobs, of a size of four to six amino acids, for sequences lacking proline residues), the charge asymmetry of each i segment was calculated as:

$${\sigma }_{\dot{i}}=\frac{{\left(f_{+}-f_{-}\right)}_i^2}{{\left(f_{+}+f_{-}\right)}_i}$$

(1)

The squared deviation of asymmetry was obtained as:

$$\delta =\frac{{{\displaystyle \sum }}_{i=1}^{N_{blob}}{\left({\sigma }_i-\sigma \right)}^2}{N_{blob}}$$

(2)

Finally, κ was defined as the ratio between δ and the maximal value for a given amino acid composition δ_max (κ = δ/δ_max). The minimum value of κ is 0, obtained when opposite charges alternate one by one. The maximum value of κ is 1, accessible to polyampholytes entirely composed of charged residues, when opposite charges are segregated into two clusters. In the seminal Pappu’s work, 30 synthetic variants of a neutral 50-mer (NCPR = 0) were designed to share an identical amino acid composition—(Glu-Lys)₂₅—but different κ values (0 ≤ κ ≤ 1), by permutations of oppositely charged residues [25]. The so-called (Glu-Lys)₂₅ system of sequences was analyzed using all-atom MC simulations applied to the Flory’s random-coil model [42,43], showing that their ensemble-averaged R_g values inversely correlate with κ [25,32]. Overall, uniformly distributed charges (κ = 0) cause expanded conformations, whereas maximal segregation of oppositely charged residues (κ = 1) results in more compact structures. Calculation of the κ value can be performed for any protein sequence through the web server CIDER (Classification of Intrinsically Disordered Ensemble Regions) (http://pappulab.wustl.edu/CIDER/), developed by Pappu’s lab [11].

Ghosh’s work, instead, tackled the charge decoration issue from a more analytical perspective, introducing a general formalism to describe heteropolymer configurational properties, in the light of sequence specificity [44]. Following the coarse-grained approach introduced by Muthukumar [45], Sawle and Ghosh described pairwise, intra-chain, and short- and long-range interaction forces, taking into account charge patterning by the “sequence charge decoration” parameter (SCD), defined as:

$$SCD=1/N[{\sum }_{m=2}^N{\mathsf{\Sigma }}_{n=1}^{m-1}{q}_m{q}_n{\left(m-n\right)}^{\frac{1}{2}}],$$

(3)

where m and n are the sequence positions within a N-mer chain, and q_m and q_n are the residue charges at those coordinates.

Similarly to κ, the SCD value tends to 0 in polypeptide sequences with uniformly distributed opposite charges. Unlike κ, the absolute value of SCD increases not only with charge segregation but also with polymer size and is ≤0 (SCD = 0 for perfectly alternated positive and negative charges). The correlation between κ and SCD, assessed on the (Glu-Lys)₂₅ system, is linear, with R₂ = 0.95 (Figure 2). Plotting the simulated R_g values [25] against κ or SCD suggests that the correspondence between R_g and SCD is even more effective than between R_g and κ, although there is no relationship between Sawle and Ghosh’s formalism and the MC simulations employed for R_g computation. The better performance of SCD could depend on the fact that this parameter takes into account all pairwise interactions, regardless of the residue position, while the κ parameter is computed by averaging over stretches of few consecutive charges (blobs) [46]. Nevertheless, Ghosh’s formalism is not well suited to describe collapsed globules (e.g., the model overestimates R_g), possibly due to the employed value of the dielectric constant or to neglecting hydrogen-bonding and ionization equilibria in the model [44,46].

Ghosh’s model has been implemented recently, to account for collapsed globules and coil–globule transitions [33]. Herein, the mathematical formalism relies on minimization of Firman and Ghosh’s free energy (βF), which allows chain conformational properties to be inferred. Moreover, Ghosh’s analytical model was applied to predict the size distribution from the whole DisProt database [47,48,49], revealing significant size differences, even among IDPs with similar FCR values (Firman and Ghosh, 2018). This result is illustrated by a phase diagram, showing the average normalized protein size in the f₊ − f₋ space (Figure 1d). Here, each bin of the heat map corresponds to an (f₊, f₋) class, for which the average value of the chain expansion parameter x at 300 K is given. The chain expansion parameter is defined as:

$$x=R_{ee}^2∕R_{ee,frc}^2$$

(4)

where R_ee is the end-to-end distance of the protein of interest and R_ee,fcr is that in the Flory random coil limit (in the absence of any interaction) of the same length. Higher values correspond to darker colors of the scale. The observation that proteins with similar values of f₊ and f₋ are predicted to have different degrees of compactness further confirms that FCR is not per se sufficient to predict chain compactness. Charge decoration, instead, as captured by Ghosh’s model, seems to account for the main sequence determinants of chain conformation.

Moreover, the same analytical model predicts different responses to salt concentration for proteins with similar FCR, highlighting once again the role of charge patterning as a determinant of the conformational behavior of polypeptides [50] (see also below in the next section).

To conclude, according to Pappu’s and Ghosh’s models, charge patterning effectively captures sequence specificity among polypeptide chains that are identical in terms of length, composition, and net charge. In this context, the overall number of charged residues (i.e., FCR) and their pattern seems to act synergistically, and independently of NCPR, to determine conformational properties of polyampholytic IDPs.

3. Relevance of Electrostatic Charges in Compaction/Expansion

Charge density and distribution deeply affect conformational states and their transitions, being modulated by pH and salt, as experimentally demonstrated [29,51,52]. The effects of salt in weakening both attractive and repulsive interactions had been well-established previously from a theoretical point of view. According to Debye-Hückel’s theory of charge screening and Higgs and Joanny’s polyampholyte theory [20,53,54], salt addition is expected to produce either conformational expansion within polyampholytes (in which attractive forces are prevalent) or increased compactness within polyelectrolytes (in which repulsive forces prevail). This section provides an overview of experimental investigations depicting the role of charge density and charge patterning on IDPs compactness.

3.1. Effects of Charges and Their Screening on Collapse/Expansion Transitions

Charge-mediated conformational transitions rely on both the effective ionization state and solvent exposure of charged residues. The contribution of electrostatics to compactness has been evaluated performing experiments at increasing salt concentrations by single-molecule Förster resonance energy transfer (smFRET), allowing the measurement of molecular distances in the range of 1–10 nm between fluorescence tags in individual proteins. Seminal studies on IDPs have explored the response of polyelectrolytes, such as the C-terminus of ProTα (ProTα, residues 52–111; FCR = 0.700, |NCPR| = 0.533) and the N-terminal domain of HIV-1 integrase (IN, residues 1–56; FCR = 0.267, |NCPR| = 0.067), to 1 M KCl, resulting, respectively, in a 30% and 10% reduction of R_g compared to the absence of salt [51]. The compaction effect, overall ascribable to the attenuation of electrostatic repulsions, depends on the net charge, being more remarkable for stronger polyelectrolytes, according to polyelectrolyte theory [50]. A subsequent systematic study on the N-terminus (residues 1–90) of the Saccharomyces cerevisiae cyclin-dependent kinase inhibitor Sic1 (hereafter called “Sic1”) has provided insights into this phenomenon, also suggesting its complexity [55]. Sic1 contains 11 positively charged residue (FCR = 0.122, i.e., 12% of charged residues) and is a weak polyelectrolyte. Figure 3a shows the results of its salt titration monitored by smFRET, with increasing KCl concentrations progressively reducing Sic1 size. Although monotonic, the composite trend of the experimental curve hints to the contribution of several phenomena, which possibly include the different accessibility to the solvent of charged residues and their different response to salt, and the influence of hydrophobic interactions, which prevail upon charge neutralization. Noteworthy, Sic1 undergoes an overall 40% reduction of its R_g in the presence of 1 M KCl. Sic1 compaction is greater than that observed for ProTα (−30%), in spite of a lower |NCPR| (0.122) than that of ProTα (0.533). How to explain the unexpectedly marked compaction of Sic1? Sic1 is a uniformly charged polyelectrolyte (FCR = |NCPR|), while ProTα, as well as IN, are “partial polyampholytes”, as indicated by the non-null difference between their FCR and |NCPR| values. Thus, the strong compaction effect elicited by salt in Sic1 can be explained by repulsion screening and a lack of swelling effects, which likely occurs in ProTα and IN because of the presence of annealed charges. Thus, NCPR and FCR cannot individually explain salt dependence, which is better rationalized by taking into account the balance between attractive and repulsive forces.

When attractive forces are predominant, it is foreseeable that salt induces conformational swelling. Clear examples of this behavior are offered by IDRs belonging to human Myc (residues 353–434), MAX (Myc-associated factor X, residues 22–102), MAD (Mitotic spindle assembly checkpoint protein MAD1, residues 55–136), MLX (Max-like protein X, residues 128–215), and MONDOA (MLX-interacting protein, residues 718–797) [56]. Such highly charged polypeptides (0.3 < FRC < 0.4) behave more markedly as polyampholytes (0.05 < |NCPR| < 0.11), with “annealed” charges conferring compact conformation in the absence of salt. When exposed to low salt concentrations (up to 0.6 M KCl), the screening of attractive interactions causes R_g expansion (Figure 3b) [56]. Above 0.6 M, a chain re-collapse is observed, probably due to hydrophobic interactions, which prevail upon charge screening. Noteworthy, different salts, e.g., LiCl, NaCl, and CsCl, cause compaction to different extents. This salt specificity is reminiscent of the variable salting-out effect along the Hofmeister series and led to the hypothesis that similar factors come into play [56].

For the sake of completeness, it is necessary to mention that several studies on polyelectrolytic IDPs have employed the denaturing salt guanidinium chloride (GdmCl), although its behavior likely reflects the overlapping effects of charge screening, preferential solvation, and chaotropic effects, especially at high concentrations [57].

To conclude, NCPR and FCR are useful parameters to roughly predict whether an IDP behaves as a polyelectrolyte or a polyampholyte in its response to salts, within the general frame provided by Debye-Hückel’s theory, and the polyelectrolyte and the polyampholyte theories. More recently, it has been proposed that chain expansion or compaction induced by salt depends also on charge patterning [50]. An experimental assessment of this theory is given by the different salt sensitivity of protein permutants obtained by simply varying the position of charge residues (“κ variants”) [58] (see Section 3.3). Understanding how environmental conditions affect IDP compactness will contribute to rationalize their function in the cellular context. This knowledge can be exploited also to better control the performance of IDP-based biomaterials and devices [50,59].

3.2. Exploitation of Charge Patterning in Stimuli-Sensitive Biopolymers

In the field of material sciences, linear polymers designed for the fabrication of solid surfaces are referred to as “polymer brushes” and have been exploited, for instance, to confer anti-biofouling and anti-frictional properties [60]. IDP-inspired polyampholyte brushes reversibly undergo expansion/collapse transitions in response to external stimuli (i.e., pH, ionic strength, temperature), consistently with their FCR and NCPR [61,62]. IDP brushes profit from a large repertoire of building blocks (i.e., canonical and unnatural amino acids) and, as typical for proteins, offer multiple hierarchical levels of structural organization dependent on their primary structure and post-translational modifications [63]. For these reasons, synthetic IDPs combine the advantages of synthetic polymers and polypeptides.

A fine example of stimuli-sensitive protein brush has been developed by Kumar’s group [59]. A recombinant IDR, rNFH-SA, derived from the heavy subunit of the rat neurofilament complex [64], was grafted in an oriented manner onto a quartz support to functionalize its surface. rNFH-SA is a highly charged polyampholyte, as inferable from its FCR (0.429) and |NCPR| (0.014) values. In addition, our analysis on charge patterning (κ = 0.074) suggests that rNFH-SA may display an expanded conformation. This protein behaves as a polymer brush capable of swelling and collapsing in response to changes in solution pH and ionic strength, in a rather wide dynamic range, not yet fully explained in the light of the theory illustrated in the previous paragraph [59]. Overall, rNFH-SA behaves as qualitatively expected for weak polyelectrolytes, which collapse with increasing salt concentration. A deeper knowledge of polyampholyte electrostatics (charge density and patterning) and of polymer physics could further help in developing “smart biomaterials” with desired properties and capable of complementing the array of already available organic/synthetic polymers.

3.3. Effects of Linear Charge Patterning over Protein Compaction

Theoretical studies on charge-decoration and its impact on polyampholyte conformation have been supported by experimental investigations. A plethora of orthogonal biophysical techniques have been employed to explore this dependence. To cite an instance, Tedeschi and collaborators carried out a systematic comparison between three κ-variants for two ~100-residue viral IDPs, merging evidence from SAXS, size-exclusion chromatography (SEC), and limited proteolysis [65]. For each protein, which displays similar values of FCR (~0.3), |NCPR| (<0.05), and κ (~0.2), the authors designed two sequence permutants, shuffling the charged residue positions in order to achieve the highest and lowest possible κ values (average values over the different proteins: κ_min~0.08 and κ_max~0.42) compatible with their natural amino acid composition while keeping the location of non-polar residues unchanged. By doing so, the conformational variability of the variants, relative to the wild-type form, could only be imputable to charge-patterning changes. A direct correlation between κ and protein size was observed. In addition, the study provided hints suggesting that differences in protein responsiveness to charge clustering also reflect differences in proline content (which is indeed different in the two model IDRs considered in that study). In particular, proline residues seem to counteract the compaction effect exerted by charge segregation.

A similar approach, yet enriched in further insights into biological implications, was used by Kriwacki and co-workers and applied to the C-terminal domain of the human cell-cycle inhibitory protein p27^Kip1 (residues 96–198, hereafter called “p27”), integrating computational simulations and biophysical techniques [66]. The authors kept the primary p27 phosphorylation site (Thr187) unmodified, altering the charge distribution around it, to lower (lowest κ value = 0.14) or increase (highest κ value = 0.78) the κ value relative to the wild-type protein (0.31). Thus, besides the expected κ–R_g inverse correlation, assessed by atomistic simulations and in-bulk conventional techniques (SAXS), the authors could also document differences in phosphorylation efficiency that could be ascribed to sequence-encoded features. Indeed, the efficiency of Thr187 phosphorylation increases with the “local” NCPR of the so-called auxiliary motifs (residues 100–180) [66], highlighting the relevance of linear charge patterns in supporting (or contrasting) a primary physiological function.

An even finer, yet consistent, characterization of p27 sequence permutants (κ values of 0.14 and 0.56) was performed by Barran’s group, exploiting native mass spectrometry coupled to ion mobility, a valuable technique to interrogate IDP/IDP ensemble conformational heterogeneity [67]. Collisional cross-sections of the permutants proved that charge patterning dramatically affects IDP/IDR compactness, with the high-κ variant displaying a lower conformational heterogeneity, compared to the wild-type and low-κ variant [58]. The latter turned out to be insensitive to increasing salt concentrations, whereas the high-κ variant displayed a conformational expansion at high ionic strength [58].

Other insights into the functional relevance of charge patterning have been obtained for RAM (RBP-Jk-associated-molecule) region, a 111-residue IDR belonging to the intracellular domain of the Notch receptor (NICD) and involved in a transmembrane cell-to-cell pathway controlling cellular differentiation and stem-cell fate [68]. The limited dispersion of κ values among distantly related RAM orthologues led to lay the hypothesis that its charge patterning responds to a functional requirement, i.e., mediating its binding affinity for CSL, an element of the tertiary complex (NICD-CSL-MAML) involved in Notch activation. Among RAM charge permutants, it was observed that R_g and an affinity for CSL decrease with increasing charge segregation, causing a significant loss in Notch transcriptional activation. Thus, experimental and computational data consistently suggest that charge decoration influences the conformational preferences of IDPs and can be considered as an evolutionary-selected trait of crucial importance for their functions.

4. Relevance of Electrostatic Charges in Protein Solubility/Aggregation and Fibrillation

Protein solubility corresponds to the ability of a polypeptide chain to dissolve into a solution, notably aqueous, and is governed by the competition among chain–solvent, inter-chain, and chain–chain interactions. Such labile equilibrium is severely impacted by solvent, ionic strength, temperature, and pH. Typically, at pH values higher or lower than the protein pI, protein–protein interactions are disfavored, in favor of chain–solvent ones, therefore increasing its solubility. Recent studies suggest that the correlation between protein pI and the pH of their (sub)cellular environment is simply a neutral “by-product” of the main adaptive selection aimed, instead, at favoring structural metastability [69]. In analogy with this original view, it could be hypothesized that protein solubility is the result of a trade-off between metastability and biological activity.

The issue of protein solubility has been widely addressed by physical statistics, considering the polymer–solvent interaction parameter χ [70,71] and polymer–solvent interaction energy. Briefly, χ can be considered as a measure of solvation enthalpy, namely the enthalpy associated with transferring the polymer from the gas phase into water. Therefore, a distinction can be drawn between “good” (χ < 0) and “poor” (χ > 0) solvents, regarding the ability to solvate a given polymer. Polymers expand and dissolve in a good solvent, while they collapse in a poor one. Referring to polypeptide chains, the propensity to be solvated depends on both backbone and side chains. Although in aqueous media the protein backbone is prone to collapse, it is the interplay among the sidechains, backbone, and solvent that decides the actual solvation fate of a protein and could support or reverse the intrinsic backbone-compaction propensity [37]. Thus, sequence specificity could account for the divalent nature of water, being a poor solvent for globular folded proteins and a good one for IDPs [37].

A plethora of predictive programs have been developed to infer aggregation propensity from the primary structure [72,73]. The next section will focus on the role of electrostatic charges in determining IDP solubility and aggregation properties.

4.1. Effects of Charge Density on Protein Solubility/Aggregation

The effect of electrostatic charges on protein solubility is controversial. Modulating protein conformation and solvation through the manipulation of pH-sensitive groups represents an exciting challenge [74,75,76], limited in practice by the difficulty of producing well-folded charge variants of globular proteins. The high designability of IDPs [77], herein meant as the number of sequences encoding conformational ensembles of similar compaction properties, is exploitable to conceive synthetic solubility-enhancing tags [78]. Solubility-enhancing tags can promote solubilization through a dual mechanism: (i) By increasing the relative proportion of solubility-enhancing amino acids with respect to the overall residue composition of the fusion construct [79]; and (ii) by acting as “entropic bristles” (EBs) through random movements around their point of attachment. EBs entropically exclude the contact with large particles, i.e., other proteins/peptides, thus reducing the probability of the fusion protein to undergo aggregation, without excluding small molecules, such as water, salts, metals, or cofactors, which in fact increase solubility [80].

A first effort to prove IDPs as effective solubility tags was performed by Santner and collaborators, who compared the solubilization performances of four synthetic intrinsically disordered tags to those of several well-established folded tags [81]. In this pivotal work, polyelectrolytes of different lengths (60, 144, 250 residues) and net charge (−24, −25, −41, and −65) yet similar pI (from 2.5 to 3) were tested. Interestingly, the chain length turned out to be more crucial than the sequence composition, with larger proteins being more effective EBs [81]. It should be emphasized that the proteins selected in this study, although presenting diverse net charges, have a seemingly high charge density, i.e., NCPR values (~−0.40; −0.29; −0.26). Therefore, the chain length, rather than the charge density, represents the most significantly diverse parameter among the analyzed proteins, without ruling out any contribution of charge density itself.

This issue was more directly addressed through a set of synthetic IDPs derived from the N-terminus moiety of measles virus phosphoprotein (PNT, 230 residues) [82], whose sequence naturally possesses an acidic pI (4.88) and an almost balanced set of oppositely charged residues, thus resulting in an NCPR ~0 (−0.071). PNT synthetic variants have the same length, FCR (0.257 ± 0.004), and hydropathy score (3.826 ± 0.067), yet they display different NCPR values (from −0.248 to +0.216) and therefore different pIs (from 3.37–9.61) [83].

As expected, each synthetic protein experiences a solubility loss at its pI. Furthermore, the “aggregation intensity”, namely the proportion of insoluble protein, turned out to be directly correlated to |NCPR|, with low-NCPR proteins remaining mostly soluble and almost aggregation free, independently of pH. PNT variants more responsive to pH are able to “transmit” their aggregation propensity to resilient proteins, such as green fluorescent protein, embedded in the same chimeric construct [83]. Overall, these observations may contribute to understanding the behavior of IDPs in response to events affecting protein NCPR (i.e., post-translational modifications, mutations, environmental changes). For instance, it could be argued that high-NCPR proteins (i.e., polyelectrolytic IDPs) are much more sensitive than polyampholytes to even slight pH changes. Results from [83] have led to the development of an empirical equation suitable to predict pH-dependent aggregation of amyloidogenic IDPs and, hence, to promote the design of synthetic solubility/aggregation tags, as well as reversibly aggregating nanofibrillar materials [84].

4.2. Relevance of Electrostatic Charges on Fibrillation

Amyloid fibrils have been associated with important biological functions [85,86] and a plethora of pathologies, including socially relevant neurodegenerative diseases, such as Alzheimer’s and Parkinson’s diseases [87]. Aggregation can be triggered in proteins, as the result of either “ordering” of disordered regions or “disordering” of well-folded structures [88]. For a more detailed description of fibril structure, see Appendix B. The research on the “amylome”, the ensemble of amyloidogenic proteins in a proteome, has indicated that most proteins can form amyloid fibrils in vivo [89], with the involvement of different sequence features. Most frequently, canonical amyloid fibrils are encoded by stretches of 5–15 residues of aliphatic and aromatic amino acids (Riek, 2018). Nevertheless, the aggregation of prions and prion-like domains is apparently independent of aliphatic residues and influenced by pH [90,91,92]. In this subclass of amyloids, which are self-perpetuating and infectious, sequence determinants have been elusive for years, since cryptically encoded by rather long (at least 60 residues) and disordered sequences, containing a few amino acid types (i.e., low-complexity regions) rich of Tyr, Gly, and polar residues (mostly Gln and Asn) [90,93,94,95], which argue for the involvement of hydrogen bonds, van der Waals, and π–π stacking interactions [96,97,98]. Short linear sequence motifs rich in polar residues (e.g., SYSGYS from human FUS protein, or GNNQQNY from yeast Sup35) have also been recognized as “nucleation centers” or “soft-amyloid cores”, effectively promoting both spontaneous and seeded aggregation in proteins [99,100], and natural and synthetic peptides [101,102,103].

The structures of human prion protein (PrP) fibrils, recently solved by Cryo-electron microscopy (Cryo-EM), have clarified the role of hydrophobic, polar, and charged residues [104,105]. The fibrils obtained from residues 23–231 of human PrP display a hydrophobic and compact core stabilized by an intramolecular disulfide bond (between Cys179 and Cys214), while a mostly hydrophilic surface is exposed to the exterior. Indeed, each fibril consists of two protofibrils intertwined in a left-handed helix, with Lys194 and Glu196 from opposing subunits forming salt bridges and creating a hydrophilic cavity at the interface of the two protofibrils [105]. This structure is coherent with previous data suggesting the critical role of pH in promoting prion fibrillization [92].

As concerning canonical amyloid fibrils, polar and charged residues are frequently arranged in disordered protrusions at the fibril edges of the hydrophobic fibril core, being functional to elongation through transient interactions with incoming monomers [106]. Such flexible charged structures have been detected, for instance, in the aggregation products of α-synuclein, Aß peptide, and tau protein [106]. Nonetheless, electrostatic interactions can also play a direct role stabilizing the cross-β-sheet structure. In this respect, we summarize here available data on the impact of charge decoration and electrostatic networks in α-synuclein (α-Syn) fibrillation, generally regarded as the pathological hallmark of Parkinson’s disease [107,108] and other synucleinopathies [109,110]. Charge density and, ante litteram, charge segregation of α-Syn have been deeply investigated for their effects on fibrillation. α-Syn is an IDP composed of 140 residues (FCR = 0.279; NCPR = −0.064; κ = 0.172) containing an N-terminal domain with a highly conserved α-helical-prone lipid-binding region (residues 1–60), a central hydrophobic region (NAC) essential for α-Syn aggregation (residues 61–95). and a C-terminal tail (residues 96–140), acting as an interaction hub for several proteins [111,112,113,114,115] (Figure 4a). The NCPR profile calculated by CIDER (Figure 4b) suggests a sharper distinction between an amphipathic and amphoteric N-terminal moiety (residues 1–102), in which opposite charges alternate almost regularly (κ = 0.082; FCR = 0.311), and a highly acidic C-terminus (residues 103–140) with highly clustered negative residues (FCR = −0.368). In vitro fibrillation of α-Syn is markedly pH dependent and occurs at higher rates at acidic pH [116,117]. This acidification effect can be explained considering the α-Syn domain structure. Indeed, acidification increases the net charge of the N-terminal moiety (from +6 at neutral pH to +17 at pH 3) and neutralizes the negative charge of the C-terminal domain (from −15 at neutral pH to 0 at pH 3). Albeit this transition involves a similar number of charged residues in each protein moiety (+17 at the N-terminus and −15 at the C-terminus), the N-terminal region at an acidic pH displays a markedly lower charge density (local NCPR_1–102 = +0.17) than the C-terminal domain at neutral pH (local NCPR_103–140 = −0.39). Such a reduction in charge density weakens intra- and inter-molecular electrostatic repulsions, as well as solvent interactions, and ultimately enhances hydrophobic interactions responsible for fibrillation [116,117].

The role of the C-terminal tail in pH-driven fibrillation of α-Syn has been further supported by experimental [122] and computational studies [123]. Data reported so far depict the C-terminal domain as an effective EB. As long as it is highly charged, expanded. and capable of large conformational fluctuations, it acts as an intramolecular chaperone, counteracting aggregation. The N-terminal region, instead, populates an ensemble of unfolded conformations with some intrinsic helical propensity, in equilibrium with membrane-bound, monomeric and multimeric, and helical structures [118,124,125] (Figure 4a). Cryo-EM studies indicate that the fibril core of α-Syn consists of residues 37–99, while the N- and C-terminus remain flexible and not resolved. The structural detail of fibrils indicates the key role of a network of electrostatic interactions involving intramolecular (i.e., E46-K80, K58-E61) and intermolecular salt bridges (K45-E57) (Figure 4c) [120]. The analysis of the E46K variant, associated with a severe form of familial Parkinson’s disease, highlights the importance of electrostatic interactions in defining the fibril morphology, as well. Indeed, with respect to the wild type, the E46K variant reshapes the above-mentioned electrostatic network, and forms a smaller fibril core (residues 45–99) and a distinct fold. This is of utmost relevance with regard to the pathogenic mechanism, as E46K fibrils are less resistant to proteases and mechanical stress and, therefore, more prone to propagation [121].

As expected from a role of electrostatic interactions in fibrillation, salts affect the aggregation kinetics of amyloid proteins. However, they do that in a highly complex way. A systematic analysis of the effect of salts on protein aggregation kinetics has been performed by testing ions from the Hofmeister series in real-time quaking-induced conversion assays [126]. This study reveals different effects of ions, depending on their position in the Hofmeister series, in line with a crucial role of protein hydration in fibril formation [127]. The effect is more remarkable for anions than cations and dependent on the biological matrix. Furthermore, the dependence of aggregation kinetics on Hofmeister ions is highly protein specific. The PrP and tau have opposite trends along the series, while α-Syn displays a bimodal response, with enhanced kinetics at both ends of the series. These results are in line with a complex interplay of electrostatic, hydrophobic, and hydration effects governing protein fibrillation and with the involvement of specific residues of different nature in these proteins.

5. Relevance of Charge Decoration in Phase Separation

Spatio-temporal control of intracellular reactions is based on a finely regulated molecular trafficking through cellular compartments. Besides membrane-limited structures, membrane-less organelles [128,129,130] contribute to compartmentalization, separating molecules by liquid demixing and confining them in droplets at higher local concentrations than the surrounding matrix [131,132], thereby creating dynamic proteinaceous microreactors [133] (see Appendix C). LLPS can occur through heterotypic (i.e., interaction and de-mixing of two or more polymers) or homotypic coacervation (i.e., single-polymer self-association) [134,135]. Coacervation usually occurs at concentrations and temperatures thermodynamically favoring self-interaction of polymers. Biomolecular condensates are generally enriched with multivalent molecules prone to establishing multiple intra-chain and interchain interactions [128]. Therefore, proteins with a modular architecture, encompassing low-complexity regions and/or repeats of short-linear motifs, are particularly well suited to nucleate coacervation. It is therefore not surprising that IDPs/IDRs display a strong propensity to undergo LLPS.

Different types of non-covalent interactions have been implicated as triggering factors: Hydrogen bonding, cation–π contacts, electrostatic and dipolar attractions, and π–π interactions between aromatic rings [128,136] (see also Appendix C). Our understanding of sequence determinants of phase behavior is in its infancy and we have just started learning its “grammar” [136,137]. Aromatic residues (Phe, Tyr), along with charged ones (Arg in particular), have often been shown to be key determinants of in vivo and in vitro LLPS occurring through short-range attractive forces due to π–π or cation–π interactions [134,136,138,139,140,141,142]. Fewer studies have investigated long-range electrostatic interactions between charged residues and their patterning on LLPS [46,139,142], although they might have a prominent role, due to the compositional features of IDPs [143]. To assess the role of electrostatic interactions, experiments are typically carried out in the presence of varying concentrations of salt, most often represented by NaCl. A seminal work on the N-terminal domain of Ddx4 (Ddx4^N), a primary constituent of human germ granules, has unveiled that its coacervation is dominated by π–cation interactions involving Phe and Arg residues. The LLPS of Ddx4N is hence extremely sensitive to ionic force, as highlighted through experiments at increasing concentrations of NaCl [134].

Two other illustrative examples are provided by hnRNPDL and NPM1, which are involved in a form of muscular dystrophy and in the spatial organization of the nucleolus, respectively. HnRNPDL (and its isoforms) was found to only form liquid-like droplets at low ionic strength [144], and homotypic LLPS of NPM1 is similarly impaired at high NaCl concentrations [145]. Overall, these behaviors are consistent with the polyampholyte theory and with the hypothesis that LLPS is driven by the annealing of opposite-sign charges or by cation–π interactions.

In contrast with the three examples above, the N-terminal prion-like domain of galectin-3 undergoes LLPS only when the NaCl concentration is increased above 600 mM, with LLPS being driven by π–π interactions between aromatic residues [146].

Examples also exist where salt, namely NaCl, does not exert any significant impact on LLPS, suggesting that the formation of coacervates relies on hydrophobic interactions. An illustrative example is provided by PNT3, a viral protein region that undergoes LLPS with concomitant formation of amyloid-like fibrils [147]. Although this protein is classified as a strong polyampholyte (FCR = 0.364, |NCPR| = 0.164), NaCl does not affect its ability to form aggregates (at least up to 300 mM). In support for the hypothesis of the involvement of π–π interactions, the most amyloidogenic region contains three contiguous tyrosine residues whose replacement with alanine residues abrogates fibrillation [147]. Finally, we can cite the case of γ44-gliadin, a wheat storage protein with an intrinsically disordered domain that undergoes LLPS in a salt-dependent manner in spite of its very weakly charged nature (FCR = 0.04 and NCPR = 0) [148]. In particular, increasing NaCl concentrations were found to lead to a drastic decrease in the number of droplets and to an increase of γ44-gliadin saturation concentrations, corresponding to equilibrium concentrations above which phase separation occurs in in vitro experiments. This behavior argues for a contribution of electrostatic interactions in the formation of γ44-gliadin liquid-like droplets. Since the few charges are mainly located in the C-terminal domain, the authors proposed that this unequal charge distribution along the sequence likely promotes directional interactions: Aromatic residues of the N-terminal domains and positively charged residues of the C-terminal ones could participate in LLPS by π–cation interactions, as already reported [134,149,150].

The relentless tug of war between electrostatics and the hydrophobic effect is also a determinant for the link between aggregation and LLPS. To cite an instance, a connection between aggregation and LLPS of tau protein has for a long time been suggested [151,152,153] and recently ruled out [154]. For tau protein, LLPS is driven by complex coacervation mechanisms, dominated by long-range multivalent electrostatic attractions [155]. Instead, the amyloidogenic pathway seems driven by hydrophobic interactions [154]. In line with the behavior of tau, in the case of hnRNPDL, LLPS exerts a protective role against fibril formation [144]. On the contrary, when LLPS is triggered in vitro under high-salt concentrations, thereby becoming partially driven by hydrophobic contacts, a direct correlation with increased amyloid propensity is observed, suggesting that this two phenomena not only could occur under coinciding conditions but could also positively influence one another [154].

Although we can try to rationalize these complex responses, we are still far from acquiring the ability to predict them. The emerging scenario from the available literature data is that the effect of salt on LLPS is poorly predictable and highly protein dependent, analogously to its impact on protein fibrillation (see Section 4). This lack of a clear trend may depend on the double role of charged residues in the so-called architecture of “stickers” and “spacers” [141,156,157]. Stickers are protein motifs or domains reversibly interacting with other protein molecules or nucleic acids, thus creating coacervate networks. Spacers are located between stickers and preferentially interact with solvent molecules, acting as a scaffold [141,156,157]. In contrast with aromatic residues, which are definitely enriched in stickers’ elements, charged residues could play a role either in stickers, by electrostatic attractions, or in spacer regions, by conferring solubility and flexibility to the scaffold itself. This ambiguity can also entail the difficulty of designing electrostatically driven LLPS models with predictable and controllable behavior [142].

An even smaller number of studies deal with the role of charge distribution in LLPS. Coacervation was found to strongly depend on the segregation of opposite charges in the Ddx4^N and Nephrin intracellular domain, which also a share similar value of κ (= 0.237 and 0.217, respectively) [134]. For instance, LLPS was suppressed by attenuating charge segregation in Ddx4^N in a permutant with κ = 0.053 [134]. A systematic analysis of the relationship between LLPS propensity and the linear pattern of charge distribution, namely the values of κ, has been addressed by computationally predicting the phase diagrams of (Glu-Lys)₂₅ by a random-phase approximation approach [46]. Overall, the system shows a binodal curve with an upper critical temperature of coacervation (see Figure A2), which correlates well with κ. Since Rg decreases with increasing κ, a power law linking R_g to the critical temperature (CT) holds as well [46]. Thus, the more compact the conformation, the higher the critical temperature, which is overall consistent with experimental evidence [134,158]. We propose, however, the existence of a “compaction threshold”, above which the dependence of CT on κ is inverted. That is, compaction would promote phase separation up to a certain limit, beyond which highly collapsed conformations would instead disfavor inter-chain interactions. In our hypothesis, IDPs/IDRs with low-to-moderate κ values display a higher propensity to undergo LLPS, while those containing interspersed charged residues (κ~0), as well as those with highly segregated charges (κ~1), present a lower coacervation propensity (Figure 5, top panel). To test this hypothesis, IDRs from the PhaSePro database [159] undergoing electrostatically driven phase separation were analyzed herein to extract a κ-value distribution. Each frequency class was compared with that of IDRs from the entire DisProt database. As shown in Figure 5, the frequency of sequences with 0.2 < κ < 0.25 in PhasePro is double compared to DisProt. By contrast, the frequency of sequences with 0.25 < κ < 0.3 is less than half (Figure 5, bottom panel). These data indicate that IDRs undergoing electrostatically driven phase separation have κ values mostly comprised between 0.2 and 0.25. Such κ values, as in the case of Ddx4 [66,160] and NICD [158], are those that probably allow to better exclude the solvent and favor inter-chain interactions. Nonetheless, the still limited size of PhaSePro (28 entries of IDPs/IDRs undergoing electrostatically driven phase separation at the time of this analysis) points to the need of addressing this issue in a more systematic way in the future, so as to be able to confirm the existence of an optimal value of κ favoring phase separation and possibly draw general conclusions. Our hypothesis is in line with a recent work indicating how critically important the patterning of sticking elements is, with the implication that too many sticky elements may hamper coacervation [141].

An obvious limitation in LLPS studies is that in vitro experiments cannot reproduce the complexity of the intracellular environment. Therefore, the picture needs to be further detailed, bearing in mind the peculiar features of the cellular context, in addition to simplified molecular models.

6. Conclusions

Today more than ever, knowledge concerning the role of electrostatics on the structure and function of IDPs/IDRs benefits from theoretical, experimental, and heuristic contributions from the fields of polymer physics and computational science. Tapping into such concepts has become imperative albeit challenging, as already pondered more than 20 years ago by one of the fathers of modern molecular biology [162]. Useful descriptors of IDP/IDR charge density and patterning, such as NCPR, κ, and SCD, arise from this very productive crosstalk between polymer theory, biophysics, computational simulations, and protein science, and contribute to deciphering the hidden structural code of IDPs/IDRs. The unfolded states of proteins have long been recognized as crucial models to interpret relevant biological processes, such as protein folding, membrane translocation, and stability, aided by the theoretical framework of statistical and polymer physics [163]. In this regard, IDPs/IDRs represent an interesting experimental model, as they offer significantly populated unfolded states in the absence of denaturants. One useful aspect resides in their remarkable designability and stimuli responsiveness. The high designability of disordered proteins allows for functional remodeling and modification of entire biological networks [164,165].We have learnt that such a reshaping can be obtained by tuning simple sequence parameters, such as the fraction of positive and negative charges and their clustering. The abundance and distribution of charged residues can confer specific sensitivity to changes in the environment, i.e., pH, ionic strength and ligands [56,83]. This plasticity is likely one of the reasons of their evolutionary success in regulatory networks. An interdisciplinary approach is essential for (i) a deeper understanding of the molecular mechanisms underlying physiological and pathological events, and (ii) translating our knowledge on polymers physics into de novo design of polypeptides with the desired properties of compactness, fibrillation, and phase separation, envisaging expectedly impactful biotechnological applications. Our knowledge of polymer physics does not yet allow to fully understand and especially control these events, particularly concerning phase separation, fibrillation, and their connection. This is partly due to the fact that this research field is still in its infancy. This area of research will benefit from the growth of dedicated databases, such as AmyPro [166], CPAD [167], DrLLPS [168], or PhasePro [159], and from data analysis through advanced data-mining tools, which will also become increasingly available in the future.