Relating sequence encoded information to form and function of intrinsically disordered proteins

Abstract

Intrinsically disordered proteins (IDPs) showcase the importance of conformational plasticity and heterogeneity in protein function. We summarize recent advances that connect information encoded in IDP sequences to their conformational properties and functions. We focus on insights obtained through a combination of atomistic simulations and biophysical measurements that are synthesized into a coherent framework using polymer physics theories.

Figure 1. Definitions of polar tracts, polyelectrolytes, and polyampholytes

Polar tracts shown here include polyQ (UniProt ID: P42858): Polyglutamine tracts are found in at least ten proteins associated with human neurodegenerative disorders including Huntington’s disease; Sup35 (UniProt ID: P05453): Residues 4–23 of S.cerevisiae Sup35 corresponding to a region of the N-terminal prion domain; EcSSB (UniProt ID: P0AGE0): Residues 117–136 of E.coli single stranded DNA binding protein corresponding to a region of the C-terminal tail; Nup42 (UniProt ID: P49686): Residues 181–200 of S.cerevisiae nucleoporin Nup42 corresponding to a region of the FG domain, which modulates gating of the nuclear pore complex. Polyampholytes shown here include: Nup60 (UniProt ID: P39705): Residues 412–431 of S.cerevisiae nucleoporin Nup60 corresponding to a region of the FG domain which modulates gating of the nuclear pore complex; PfSSB (UniProt ID: Q8I415): Residues 232–251 of P.falciparum single stranded DNA binding protein corresponding to a region of the Cterminal tail; Nsp1 (UniProt ID: P14907): Residues 359–378 of S.cerevisiae nucleoporin Nsp1 corresponding to a region of the FG domain which modulates gating of the nuclear pore complex; PQBP1 (UniProt ID: O60828): Residues 146–165 of H.sapiens polyglutamine-tract binding protein 1 corresponding to a region of the expanded linker, which connects the N-terminal WW domain and the C-terminal U5 15 kDa binding region. Polyelectrolytes shown here include: PRM2 (UniProt ID: Q9EP54): Residues 2–21 of the C.griseus DNA packaging protein protamine 2, which is involved in the chromatin condensation process during spermatogenesis [6]; PDE6G (UniProt ID: P18545): Residues 63–82 of H.sapiens retinal rod rhodopsin-sensitive cGMP 3′,5′-cyclic phosphodiesterase subunit gamma protein, which is involved in processing visual signal; NP1 (UniProt ID: O13030): Residues 5–24 of C.pyrrhogaster protamine 1 which is involved in the chromatin condensation process during spermatogenesis; RAG2 (UniProt ID: P21784): Residues 392–411 of C.griseus V(D)J recombination-activating protein 2 corresponding to a region of the “acidic hinge” which modulates DNA repair mechanisms.

Figure 2. Summary of the typical workflow used to extract quantitative CCRs and SCRs from computer simulations, in vitro biophysical experiments, or synergy between the two modes of investigation

Figure 3. Summary of readily calculated compositional parameters that help in quantitative assessments of CCRs for IDP sequences

Figure 4. Diagram-of-states classification depicting the distinct conformational classes for IDP sequences

Statistics for different regions (percentages) are from analysis of bona fide IDPs in DISPROT [61].

Figure 5. Illustrations of the impact of conserved versus altered CCRs on IDP functions

Figure 6. Calculation of κ and using it to distinguish the sequences with different linear patterns of oppositely charged residues

The top row shows how κ is calculated. The overall charge asymmetry σ is determined by the amino acid composition (see Figure 2). Each sequence is divided into n_w sliding windows and the mean squared deviation δ helps quantify the deviation of the charge asymmetry across different sequence windows vis-à-vis the charge asymmetry encoded by the amino acid composition. The value of δ is calculated for all sequence variants that correspond to the amino acid composition and this is used to evaluate the value of κ, as shown, thus ensuring that κ is bounded between 0 and 1. As an illustration of the patterning that is quantified using κ, we show the sequence of the “polar rich domain” extracted from the sequence of the polyglutamine tract binding protein PQB-P1. The bottom two rows show two de novo designed sequences designated as sv1 and sv2 for sequence variants 1 and 2. These two sequences were derived from alterations to the linear sequence distribution of oppositely charged residues [38]. On each row, the values of κ are shown to the right.

Figure 7. Illustrating the impact of sequence patterns and their conservation / alteration on IDP functions