Effects of pH and Salt Concentration on Stability of a Protein G Variant Using Coarse-Grained Models

Abstract

The importance of charge-charge interactions in the thermal stability of proteins is widely known. pH and ionic strength play a crucial role in these electrostatic interactions, as well as in the arrangement of ionizable residues in each protein-folding stage. In this study, two coarse-grained models were used to evaluate the effect of pH and salt concentration on the thermal stability of a protein G variant (1PGB-QDD), which was chosen due to the quantity of experimental data exploring these effects on its stability. One of these coarse-grained models, the TKSA, calculates the electrostatic free energy of the protein in the native state via the Tanford-Kirkwood approach for each residue. The other one, CpHMD-SBM, uses a Coulomb screening potential in addition to the structure-based model C_α. Both models simulate the system in constant pH. The comparison between the experimental stability analysis and the computational results obtained by these simple models showed a good agreement. Through the TKSA method, the role of each charged residue in the protein's thermal stability was inferred. Using CpHMD-SBM, it was possible to evaluate salt and pH effects throughout the folding process. Finally, the computational pK_a values were calculated by both methods and presented a good level of agreement with the experiments. This study provides, to our knowledge, new information and a comprehensive description of the electrostatic contribution to protein G stability.

Figure 1

(A) Structure of PGB1-QDD is built from wild-type protein with PDB:1PGB. The side chains are shown for residues that have major contributions to protein stability. (B) Shown here is the primary sequence of PGB1-QDD with highlighted acidic residues, which have the highest charge variations in the studied pH range. To see this figure in color, go online.

Figure 2

Electrostatic energy contribution to free energy native state stability ΔG_elec as a function of pH in kJ/mol. The values were calculated from TKSA simulation analysis for 23 different pH values from 1.0 to 12.0. The solid circles represent values for 0.15 M of a monovalent salt concentration in simulation and the open squares represent values of 2.0 M of salt concentration. (Inset) Plot shows the experimental results of the free energy difference between the unfolded and the native state ΔG° from 1PGB-QDD as a function of pH in kJ/mol. The solid circles represent values for 0.15 M of NaCl, and the open squares represent values for 2.00 M of NaCl (adapted from (37)).

Figure 3

Charge–charge interaction energy ΔG_qq calculated by the TKSA model for each ionizable residue. (A–D) Given here are the energy profiles of pH values 2.5, 4.5, 7.5 and 10.0, respectively. The red bars indicate the residues with the side chain exposed to solvent with SASA ≥ 50% and positive energy contribution to native state stability, most of these residues are located between D36 and E42. To see this figure in color, go online.

Figure 4

Thermodynamic properties of 1PGB-QDD folding. (A) Shown here are heat capacities at constant volume (C_v) in low, intermediate, and high salt concentrations. Solid black lines are for pH 2.5, short dashed red lines are for pH 4.5, long dashed blue lines are for pH 7.5, and dashed/dotted green lines are for pH 10.0. (B) Given here are free energy curves as a function of the reaction coordinate Q for the same three salt concentrations. All systems are at T close to T_M (melting temperature) of pH 7.5 in each ionic strength. It is considered that the melting temperature corresponds to the peak of C_v. To see this figure in color, go online.

Figure 5

Values of melting temperature T_M^∗ in reduced temperature as a function of pH. Black circles are for low salt, red squares are for an intermediate ionic strength, and blue diamonds are for high salt concentration. Inset graphic presents the experimental results of T_M^∗ as a function of pH in similar salt conditions to simulation (adapted from (37)). Dashed lines connecting symbols help guide the eye. To see this figure in color, go online.

Figure 6

2D map of the distribution of electrostatic energy as a function of the reaction coordinate Q for pH 2.5, 4.5, 7.5, and 10.0. The color map represents the probability distribution of the electrostatic energy and Q, normalized by its highest value. All the systems are at T ≈ T_M and intermediate salt concentration. The value q represents the net charge of 1PGB-QDD in each minimum. To see this figure in color, go online.

Figure 7

Titration curves of residue D22: ionization degree α as a function of pH. (A) The value α is calculated for the folded 1PGB-QDD using the CpHMD model. (B) The value α is calculated for the unfolded 1PGB-QDD via the CpHMD model. (C) The value α is calculated for the folded protein using the TKSA model. Red curves are the fit of the Hill equation (Eq. 7). To see this figure in color, go online.