Mutational effect of structural parameters on coiled-coil stability of proteins.

Understanding the parameters that influence the melting temperature of coiled-coils (CC) and their stability is very important. We have analyzed 45 CC mutants of DNA binding protein, electron transport protein, hydrolase, oxidoreductase, and transcription factors. Many mutants have been observed at Tm = 40 °C-60 °C with ΔS = 9-11 kcal/°C mol, ΔG = -400 to -450 kcal/mol, and Keq = 0.98-1.03. The multiple regression analysis of Tm reveals that influences of thermodynamic parameters are strong (R = 0.97); chemical parameters are moderate (R = 0.63); and the geometrical parameters are negligible (R = 0.19). The combination of all these three parameters exhibits a little higher influence on Tm (R = 0.98). From the analysis, it has been concluded that the thermodynamic parameters alone are very important in stability studies on protein coil mutants. Besides, the derived regression model would have been useful for the reliable prediction of the melting temperature of coil mutants.

Introduction

Among all the found coiled-coils (CC), the dimeric CC only populates 73.8%, whereas the other 26% are more complex.1 The architecture of a particular CC domain determines its oligomerization state, rigidity, and ability to function as a molecular recognition system. Much progress has been made towards understanding the parameters that determine CC formation and stability.2 As per the previous reports, by combining the most favorable inter- and intra-helical salt-bridge arrangements, it is possible to design CC oligomerization domains with improved stability properties.3 It has been concluded that dynamic changes in the helical registry may be a general property of CC.4

The hydrophobic interactions that occur along the CC interface stabilize the α-helical CC, and the hydrophobic clustering stabilizes the CC structure.5 There is preference for hydrophobic (Ala, Leu), positively- (Lys, Arg), and negatively- (Glu) charged residues in CC domains. The surrounding hydrophobicity of residues in CC domains is significantly less than that of residues in other regions of CC proteins. The residues in CC domains are more stable than those in other regions and are largely influenced by medium-range contacts. The long-range interactions play a dominant role in other regions of protein, as well as in non-CC helices.6

Stability measurements indicate that maintenance of all favorable electrostatic interactions, or the avoidance of two potentially repulsive interactions contributes approximately 2.1 kcal/mol to helix orientation preference.7 The guanidine hydrochloride (GdnHCl) masks electrostatic repulsions due to its ionic nature. In addition, Glu and Gln in the e and g positions of the heptads repeat and have very similar effects on CC stability in the presence of GdnHCl.8 Buried urea/urea contacts lead to extremely stable dimeric CC at melting temperatures between 63 °C and 79 °C. Core ureas can also form stable complexes with a variety of other polar groups, including guanidine, acids, and amides.9

Earlier studies suggest that the classified structural information is more dominant than the experimental conditions for understanding the stability of protein mutants. The comparison of amino acid properties with free-energy terms indicated that the energetic contribution explained the mutant stability better in the coil region.6 The present work discusses how different parameters influence the melting temperature of protein coil mutants. This study also reveals that whether the degree of influence be large or small, it would have some effect on coil mutant stability at different solvent accessibility.

Materials and Methods

Datasets

The dataset contains different coil mutants (289 data) of 1RN1, 1A23, 1STN, 1RGG, 1CSP, 1HUE, 1FTG, 1RX4, 1RGG, and 1C9O at exposed, partially buried, and buried regions. These proteins belong to the classification of DNA binding protein, electron transport protein, hydrolase, oxidoreductase, and transcription factors. This dataset has been generated from the ProTherm database,10 available at http://gibk26.bio.kyutech.ac.jp/jouhou/Protherm/protherm.html. The data redundancy check was carried out for reliable result prediction. The experimental data such as Tm, ΔTm, ASA (%), and pH has been obtained with conditions such as: two state proteins, single mutation, coil secondary structures, and thermal denaturation. The availability of parameters like ΔCp, activity, and so on, is insufficient to use in the present data analysis. In addition, the more significant parameters have not been ignored. Hence, the omissions of the abovementioned less significant parameters do not cause much effect on result prediction.

Amount of hydrogen atoms (pH)

The hydrogen atoms are positively charged and they attract the negative side of the polar amino acids. Some amino acids are polar and have positively- or negatively-charged side chains. Thus, the change in pH alters the stability of a protein structure.

Accessible surface area (ASA)

The solvent-accessible surface area, ASA or SASA, is often used for calculating the transfer-free energy, ΔGtr. This transfer-free energy is required to move a biomolecule from an aqueous solvent to a non-polar solvent, such as in a lipid environment. The ASA can be used to improve protein secondary structure prediction.11,12

Melting temperature (Tm)

The protein melting point is an important characteristic feature of a protein and is used for various purposes such as drug development. In general, the protein will be more stable if the Tm is high. As per the previous report, the melting temperature of a protein can be predicted from its amino acid sequence.13

Van’t Hoff analysis

The van’t Hoff equation relates the equilibrium constant with temperature, melting temperature, and standard enthalpy change of the process.

where, Keq—equilibrium constant; ΔHvH—van’t Hoff enthalpy; R—gas constant; Tm—melting temperature; and T—temperature.

Chemical thermodynamic relationships

The Tm and ΔTm values could be determined experimentally; T and Keq values can be calculated using equation 2. From equation 3, the change in free energy (ΔG) is calculated. The change in entropy (ΔS) is calculated by equation 4.

Free energy change (ΔG) and transfer-free energy change (ΔGtr)

The positive ΔG indicates that the native state is more stable than the denatured state. The hydrophobicity scale based on transfer Gibbs energy of residues from the non-aqueous phase to water has been widely used to estimate the conformational stability of proteins. As per the previous report, the molar volume-corrected octanol solubility scale provides the best agreement with changes in protein stability upon mutation.14 The solubility scale based on octanol to water transfer energies for the amino acids has been used for our analysis.

Compactness (Z)

Compactness is calculated through a solvent-accessible surface area of a fragment (ASAsurf), divided by its minimum possible area. The minimum possible surface area is the surface area of a sphere with an equal volume as that of the fragment,15 which is calculated by an integration of all individually exposed solvent-accessible surface areas.16

The ASA (Å2) values taken from ProTherm database include: Ala-110.2; Asp-144.1; Cys-140.4; Glu-174.7; Phe-200.7; Gly-78.7; His-181.9; Ile-185.0; Lys-205.7; Leu-183.1; Met-200.1; Asn-146.4; Pro-141.9; Gln-178.6; Arg-229.0; Ser-117.2; Thr-138.7; Val-153.7; Trp-240.5; and Tyr-213.7. The classification of amino acids used in this study (as given in the database) is as follows: buried if presenting an ASA with less than 20% accessibility; partially buried if the ASA is between 20% and 50%; and exposed if the ASA is more than 50%.

Coil propensity (Pc)

The propensity of amino acids for coil conformation is also an intrinsic property of amino acids. The amino acid propensities for secondary structures are more reliable depending on the degree of homogeneity of the protein dataset used to evaluate them.17

Single correlation (r) and multiple regression (R) analysis

The relationship between melting temperature and mutation-induced property changes, such as ASA, transfer free energy, van’t Hoff enthalpy, equilibrium constant, and so on, have been calculated using Pearson’s correlation. The multiple regression coefficients for all mutants are computed from all possible combinations of geometrical, chemical, and thermodynamic parameters. In addition, the regression models are derived for each category.

Results and Discussion

Coil mutations

When considering the free energy change due to mutation, many data lie in the range of ASA of 0%–80%, which is shown in Figure 1A. In Figure 1B, many mutants are found in the range of 30 °C–80 °C of melting temperature. The plot between pH and ΔΔG shows that many data are available at pH 2–3, pH 4–8, and near pH 7, and comparatively few data are also available at pH 8–10 (Fig. 1C). The correlations between ASA and ΔΔG seem to be high at pH 6–7 (Table 1). In addition, considerable amounts of van’t Hoff enthalpy values are also available for pH 7, so the relationship between Tm and ΔHvH at pH 7 at different ranges of solvent accessibility is analyzed.

Figure 1

(A) Plot depicts the relationship between ASA (%) and free energy change due to various single mutations in the coil region. (B) Plot depicts the relationship between Tm and free energy change due to various single mutations in the coil region. (C) Plot depicts the relationship between pH and free energy change due to various single mutations in the coil region.

Table 1

Relationship between accessible surface area and free energy change due to mutation at various pH ranges.

r	ASA vs. ΔΔG	Number of data
All pH	0.22	222
pH 1.1–2.0	0.49	36
pH 2.1–3.0	0.53	69
pH 3.1–4.0	−0.96	12
pH 4.1–5.0	−0.26	27
pH 5.1–6.0	0.06	34
pH 6.1–7.0	0.50	116
pH 7.1–8.0	0.01	45
pH 8.1–9.0	0.30	13
pH 9.1–10.0	0.06	13

However, multiple Tm values are found for the same entry in the ProTherm database under the same set of conditions. The collected data has been categorized into the dataset with low Tm values and the dataset with high Tm values, and appreciable correlations are not found for entries with high Tm values. So, the dataset with low Tm values is focused for further analysis, and the melting temperature shows a strong negative correlation with free energy changes. The melting temperature also gives an average negative correlation with entropy change and the equilibrium constant (Table 2).

Table 2

Illustration of various parametrical relationships with melting temperature.

Parameters	r
Tm vs. ASA	0.34
Tm vs. ΔHvH	−0.17
Tm vs. ΔS	−0.58
Tm vs. ΔG	−0.73
Tm vs. Keq	−0.59
Tm vs. ΔGtr	−0.22
Tm vs. Z	−0.19
Tm vs. Pc	0.15

The distribution of entropy change, free energy change, and the equilibrium constant-related data with melting temperature is illustrated in Figure 2A–C, in which Tm = 40 °C–60 °C consists of many data with ΔS = 9–11 kcal/°C mol, ΔG = -400 to −450 kcal/mol and Keq = 0.98–1.03. The multiple regression of Tm is high with thermodynamic parameters, average with chemical parameters, and negligible with geometrical parameters (Table 3).

Figure 2

(A) Illustration of entropy change versus melting temperature with no data redundancy. (B) Illustration of free energy change versus melting temperature with no data redundancy. (C) Illustration of equilibrium constant versus melting temperature with no data redundancy.

Table 3

Illustration of derived regression models and regression coefficients.

Sl. no.	Parameters	Regression model	Regression coefficient
1	Thermodynamic	Tm = 298.09 + 0.58ΔHvH − 31.63ΔS − 0.04ΔG	0.97
2	Chemical	Tm = 331.63 − 276.06 Keq − 0.98ΔGtr	0.63
3	Geometrical	Tm = 53.31 − 0.01Z +0.94Pc	0.19
4	Combined	Tm = 308.17 + 0.17ΔHvH − 10.78ΔS − 0.09ΔG − 199.67 Keq + 0.69ΔGtr − 0.01Z + 2.40Pc	0.98

Note: Bold data represents high correlation (>0.5).

Conclusion

Many mutants are observed at Tm = 40 °C–60 °C with ΔS = 9–11 kcal/°C mol, ΔG = −400 to −450 kcal/mol, and Keq = 0.98–1.03. The multiple regression analysis of coil mutants Tm revealed that the influences of thermodynamic parameters are strong (R = 0.97), chemical parameters are moderate (R = 0.63), and geometrical parameters are negligible (R = 0.19); however, the combination of all these three parameters (R = 0.98) exhibits slightly higher influences on Tm than the thermodynamic parameters. It has been concluded that the thermodynamic parameters alone are very important in stability studies on protein coil mutants. In addition, the derived regression model would have been useful for the reliable prediction of the melting temperature of coil mutants.