Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues

Abstract

The functions of intrinsically disordered proteins (IDPs) are governed by relationships between information encoded in their amino acid sequences and the ensembles of conformations that they sample as autonomous units. Most IDPs are polyampholytes, with sequences that include both positively and negatively charged residues. Accordingly, we focus here on the sequence-ensemble relationships of polyampholytic IDPs. The fraction of charged residues discriminates between weak and strong polyampholytes. Using atomistic simulations, we show that weak polyampholytes form globules, whereas the conformational preferences of strong polyampholytes are determined by a combination of fraction of charged residues values and the linear sequence distributions of oppositely charged residues. We quantify the latter using a patterning parameter κ that lies between zero and one. The value of κ is low for well-mixed sequences, and in these sequences, intrachain electrostatic repulsions and attractions are counterbalanced, leading to the unmasking of preferences for conformations that resemble either self-avoiding random walks or generic Flory random coils. Segregation of oppositely charged residues within linear sequences leads to high κ-values and preferences for hairpin-like conformations caused by long-range electrostatic attractions induced by conformational fluctuations. We propose a scaling theory to explain the sequence-encoded conformational properties of strong polyampholytes. We show that naturally occurring strong polyampholytes have low κ-values, and this feature implies a selection for random coil ensembles. The design of sequences with different κ-values demonstrably alters the conformational preferences of polyampholytic IDPs, and this ability could become a useful tool for enabling direct inquiries into connections between sequence-ensemble relationships and functions of IDPs.

Fig. 1.

Thirty sequence variants for the (Glu-Lys)₂₅ system. Column 1 shows the label of each sequence variant. Column 2 shows the actual sequence, with Glu residues in red and Lys residues in blue. Column 3 shows the κ-values.

Fig. 2.

Ensemble-averaged radii of gyration <R_g> for sequence variants of the (Glu-Lys)₂₅ system. Insets show representative conformations for four sequence variants. Side chains of Glu are shown in red, and side chains of Lys are shown in blue. The two dashed lines intersect the ordinate at <R_g> values expected for all sequence variants of the (Glu-Lys)₂₅ system modeled in the EV limit or as Flory random coils (FRCs).

Fig. 3.

<R_ij> profiles for sequence variants of the (Glu-Lys)₂₅ system. The red curve denotes the profile expected for (Glu-Lys)₂₅ polymers in the EV limit. The black curve is expected for an FRC, and the solid blue curve is obtained when (Glu-Lys)₂₅ polymers form maximally compact globules. For compact globules, <R_ij> plateaus to a value that is prescribed by their densities.

Fig. 4.

Numerical fits to the <R_ij> profile for sequence variant sv30 of the (Glu-Lys)₂₅ system. The red, magenta, and black curves correspond to three distinct regimes viz.: |j − i| < 2g, 2g ≤ |j − i| ≤ l_c, and |j − i| > l_c, respectively.

Fig. 5.

<R_ij> profiles for 10 naturally occurring IDPs. The legend shows the DisProt or other identifier for each sequence. The solid curves are reference profiles that are similar to those profiles described in Fig. 3. The legend shows the sequence identifiers and the combination of FCR and κ-values in parentheses. For globule formers, the values of κ have no significance, and for these sequences, the legend shows only their FCR values.

Fig. 6.

<R_ij> profiles for the WT linker from PQBP-1 and two designed sequence variants. The sequences of the WT stretch and sequence permutants are shown. The solid red, black, and blue curves correspond to <R_ij> profiles for WPP-(PQBP-1)_132–183:wt simulated in the EV limit, FRC, and compact Lennard–Jones (LJ) globules, respectively.

Fig. 7.

Diagram of states for IDPs. We focus on sequences that fall below the parameterized line (NCPR = 2.785H − 1.151), developed by Uversky et al. (43) to separate IDPs from sequences that fold autonomously. Here, H refers to the hydropathy score. Region 1 corresponds to either weak polyampholytes or weak polyelectrolytes that form globule or tadpole-like conformations (SI Appendix, Fig. S17). Region 3 corresponds to strong polyampholytes that form distinctly nonglobular conformations that are coil-like, hairpin-like, or admixtures. A boundary region labeled 2 separates regions 1 and 3, and the conformations within this region are likely to represent a continuum of possibilities between the types of conformations adopted by sequences in regions 1 and 3. Sequences with compositions corresponding to regions 4 and 5 are strong polyelectrolytes with FCR > 0.35 and NCPR > 0.3. These sequences are expected to sample coil-like conformations that largely resemble EV limit ensembles. The legend summarizes statistics for different regions based on sequences drawn from the DisProt database. The figure includes annotation by properties of sequences that have been designated as being “coils” or “pre-molten-globules” by Uversky (3) based on measurements of hydrodynamic radii. These sequences (listed in SI Appendix, Tables S3 and S4) are expected to be expanded vis-à-vis folded proteins, and our annotation shows that, indeed, all but one of the sequences is outside the globule-forming region.