Table 1. Summary of structural features and binding thermodynamics.
hnRNP A1 RRM1 | SRSF1 pseudo-RRM2 | hnRNP F qRRM1 | Tra2β1 RRM | ΔNTra2β1 | |
---|---|---|---|---|---|
5΄ RNA 3΄ § | UUAGGU | AAGGAC | AGG*G*AU | AAGAAC | AAGAAC |
Binding mode | Canonical (β-sheet) | Pseudo-RRM (α-helix 1) | quasi-RRM (Loops) | Canonical + N and C-termini | Canonical + C-terminus |
Intermolecular hydrogen bonds | 5 | 5 | 5 | 6 | 5 |
Hydrophobic interactions | 3 | 2 | 3 | 3 | 3 |
Mean ΔGobs (kcal mol−1) | −8.0 ± 0.5 | −9.9 ± 0.3 | −8.7 ± 0.2 | −8.8 ± 0.3 | −8.4 ± 0.2 |
ΔGPE/(%) | 28 | 26 | 10 | 23 | ND |
ΔGnPE/(%) | 72 | 74 | 90 | 77 | ND |
ΔCp,obs/cal K−1 mol−1 | −130 ± 27 | −338 ± 17 | −40 ± 30 | −300 ± 23 | −166 ± 40 |
ΔCpf,ASA/cal K−1 mol−1 | −96 | −90 | −164 | −348 | −263 |
ΔCpb,ASA/cal K−1 mol−1 | −84 | −10 | −29 | −131 | −115 |
§RNA sequence used in study. Nucleotides specifically recognized by the RRMs are highlighted in bold. *7-deazaguanine. ND: not determined. ΔGobs was determined by ITC in 20 mM CH3COOH, 50 mM L-arginine, 50 mM L-glutamate, 0.05% β-mercaptoethanol–NaOH pH 5.5 at different temperatures (see also Table 2). The mean ΔGobs was obtained by averaging ΔGobs across the considered temperature range. ΔGPE and ΔGnPE are the percentage contributions of the polyelectrolyte effect (ion-release) and non-polyelectrolyte effect to the overall free energy of binding at 1M Na+ concentration, respectively. To determine ΔGPE and ΔGnPE, ITC titrations were performed at 283.15 K temperature in 20 mM CH3COOH, 50 mM L-arginine, 50 mM L-glutamate, 0.05% β-mercaptoethanol–NaOH pH 5.5 and different concentrations of NaCl salt (see Figure 5A). ΔCp,obs is the observed experimental heat capacity. ΔCpb,ASA and ΔCpf,ASA are the expected heat capacities semi-empirically calculated using the bound or free conformations of the binding components, respectively.