| Literature DB >> 36234991 |
Valeria D'Annibale1,2, Donatella Fracassi3, Paolo Marracino4, Guglielmo D'Inzeo3, Marco D'Abramo1.
Abstract
Here we present a theoretical-computational study dealing with the evaluation of the pKa of the Cysteine residues in Thioredoxin (TRX) and in its complex with the Thioredoxin-interacting protein (TXNIP). The free energy differences between the anionic and neutral form of the Cysteine 32 and 35 have been evaluated by means of the Perturbed Matrix Method with classical perturbations due to both the environment and an exogenous electric field as provided by Molecular Dynamics (MD) simulations. The evaluation of the free energies allowed us to show that the effect of the perturbing terms is to lower the pKa of Cysteine 32 and Cysteine 35 with respect to the free amino-acid. On the other hand, in the complex TRX-TXNIP, our data show an enhanced stabilization of the neutral reduced form of Cys 35. These results suggest that external electric stimuli higher than 0.02 V/nm can modulate the Cysteine pKa, which can be connected to the tight regulation of the TRX acting as an antioxidant agent.Entities:
Keywords: PMM; Thioredoxin; electric field; molecular communications; pKa
Mesh:
Substances:
Year: 2022 PMID: 36234991 PMCID: PMC9570579 DOI: 10.3390/molecules27196454
Source DB: PubMed Journal: Molecules ISSN: 1420-3049 Impact factor: 4.927
Figure 1Structure of the complex TRX-TXNIP with a focus on the active site with its CXXC motif.
Helmholtz Free Energy change and pKa for Cysteine in water, Cys 32 in TRX, and Cys 35 in TRX and in TRX-TXNIP (always using as QC).
| Molecule | pKa | pKa (exp. data) | ||
|---|---|---|---|---|
| Cysteine in water | 1174.9 ± 3.9 | 8.2 | 0 | 8.3–8.8 [ |
| Cys 32 in TRX | 1147.9 ± 4.1 | 3.5 | −4.7 ± 1.0 | 5.5–10 [ |
| Cys 35 in TRX | 1147.9 ± 4.3 | 3.5 | −4.7 ± 1.0 | 7–14 [ |
| Cys 35 in TRX-TXNIP | 1161.2 ± 5.3 | 5.8 | −2.4 ± 1.1 | N.A. |
Figure 2(a) PCA analysis on the C- of TRX and TRX-TXNIP; (b) Eigenvector components analysis for the C- atoms of TRX; (c) analysis of h-bonds between Cys 35 and solvent; (d) solvent accessible surface of the active site in TRX and in TRX-TXNIP. On the right of the figure, the TRX and TRX-TXNIP complex are shown in cartoon representation.
Mean distances along the MD trajectory between Cys 35 and Cys 32, and mean solvent accessible surface of the active site (CGPC), in absence or in presence of TXNIP.
| Molecule | Distance C35-C32 (nm) | Active Site (CGPC) Exposed Surface (nm |
|---|---|---|
| TRX | 1.09 | 6.14 |
| TRX-TXNIP | 0.40 | 5.24 |
Effect of a static electric field on the Helmholtz Free Energy change and on the pKa for Cysteine 35 in TRX.
| Electric Field (V/nm) |
| Mean Dipole Moment (D) | ||
|---|---|---|---|---|
| 0.00 | 1147.9 ± 4.3 | −4.7 ± 1.0 | 0 | 311.93 |
| 0.02 | 1128.5 ± 4.20 | −8.1 ± 0.1 | −3.4 | 332.23 |
| 0.04 | 1101.2 ± 8.7 | −12.8 ± 1.7 | −8.1 | 387.08 |
| 0.06 | 1089.8 ± 4.2 | −14.8 ± 1.7 | −10.1 | 403.23 |
| 0.08 | 1064.7 ± 12.92 | −19.2 ± 2.3 | −14.5 | 470.80 |
| 0.10 | 1070.4 ± 13.7 | −17.5 ± 2.5 | −12.8 | 427.02 |
| 0.12 | 1053.8 ± 11.5 | −21.1 ± 2.1 | −16.4 | 479.36 |
Figure 3(left) PCA comparis on between TRX and TRX-TXNIP (as reported in Figure 2a); (right) PCA for the C- of TRX: no field (blue), E = 0.06 V/nm (yellow), E = 0.12 V/nm (violet).
Figure 4Comparison between the effect of electric field and temperature on Cys 35 in TRX.
Effect of the temperature on the Helmholtz Free Energy change and pKa for Cysteine 35 in TRX, in the range of 300 to 350 K.
| Temperature (K) |
| ||
|---|---|---|---|
| 300 | 1147.9 ± 4.3 | −4.7 ± 1.0 | 0 |
| 310 | 1137.5 ± 2.7 | −6.6 ± 0.8 | −1.9 |
| 320 | 1137.7 ± 3.4 | −6.7 ± 0.8 | −2.0 |
| 330 | 1155.8 ± 6.4 | −3.8 ± 1.2 | +0.9 |
| 340 | 1136.6 ± 3.5 | −6.9 ± 0.8 | −2.2 |
| 350 | 1128.3 ± 7.6 | −8.1 ± 1.3 | −3.4 |