Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand Binding
Oculocutaneous albinism type 3 (OCA3) is an autosomal recessive disorder caused by mutations in the <i>TYRP1</i> gene. Tyrosinase-related protein 1 (Tyrp1) is involved in eumelanin synthesis, catalyzing the oxidation of 5,6-dihydroxyindole-2-carboxylic acid oxidase (DHICA) to 5,6-indoleq...
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MDPI AG
2021-09-01
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| Series: | International Journal of Molecular Sciences |
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| author | Milan H. Patel Monika B. Dolinska Yuri V. Sergeev |
| author_facet | Milan H. Patel Monika B. Dolinska Yuri V. Sergeev |
| author_sort | Milan H. Patel |
| collection | DOAJ |
| description | Oculocutaneous albinism type 3 (OCA3) is an autosomal recessive disorder caused by mutations in the <i>TYRP1</i> gene. Tyrosinase-related protein 1 (Tyrp1) is involved in eumelanin synthesis, catalyzing the oxidation of 5,6-dihydroxyindole-2-carboxylic acid oxidase (DHICA) to 5,6-indolequinone-2-carboxylic acid (IQCA). Here, for the first time, four OCA3-causing mutations of Tyrp1, C30R, H215Y, D308N, and R326H, were investigated computationally to understand Tyrp1 protein stability and catalytic activity. Using the Tyrp1 crystal structure (PDB:5M8L), global mutagenesis was conducted to evaluate mutant protein stability. Consistent with the foldability parameter, C30R and H215Y should exhibit greater instability, and two other mutants, D308N and R326H, are expected to keep a native conformation. SDS-PAGE and Western blot analysis of the purified recombinant proteins confirmed that the foldability parameter correctly predicted the effect of mutations critical for protein stability. Further, the mutant variant structures were built and simulated for 100 ns to generate free energy landscapes and perform docking experiments. Free energy landscapes formed by Y362, N378, and T391 indicate that the binding clefts of C30R and H215Y mutants are larger than the wild-type Tyrp1. In docking simulations, the hydrogen bond and salt bridge interactions that stabilize DHICA in the active site remain similar among Tyrp1, D308N, and R326H. However, the strengths of these interactions and stability of the docked ligand may decrease proportionally to mutation severity due to the larger and less well-defined natures of the binding clefts in mutants. Mutational perturbations in mutants that are not unfolded may result in allosteric alterations to the active site, reducing the stability of protein-ligand interactions. |
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| language | English |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-f1a1e77aeb154ccc9cee41cab4a0e30c2023-11-22T16:05:59ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-09-0122191020310.3390/ijms221910203Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand BindingMilan H. Patel0Monika B. Dolinska1Yuri V. Sergeev2National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USANational Eye Institute, National Institutes of Health, Bethesda, MD 20892, USANational Eye Institute, National Institutes of Health, Bethesda, MD 20892, USAOculocutaneous albinism type 3 (OCA3) is an autosomal recessive disorder caused by mutations in the <i>TYRP1</i> gene. Tyrosinase-related protein 1 (Tyrp1) is involved in eumelanin synthesis, catalyzing the oxidation of 5,6-dihydroxyindole-2-carboxylic acid oxidase (DHICA) to 5,6-indolequinone-2-carboxylic acid (IQCA). Here, for the first time, four OCA3-causing mutations of Tyrp1, C30R, H215Y, D308N, and R326H, were investigated computationally to understand Tyrp1 protein stability and catalytic activity. Using the Tyrp1 crystal structure (PDB:5M8L), global mutagenesis was conducted to evaluate mutant protein stability. Consistent with the foldability parameter, C30R and H215Y should exhibit greater instability, and two other mutants, D308N and R326H, are expected to keep a native conformation. SDS-PAGE and Western blot analysis of the purified recombinant proteins confirmed that the foldability parameter correctly predicted the effect of mutations critical for protein stability. Further, the mutant variant structures were built and simulated for 100 ns to generate free energy landscapes and perform docking experiments. Free energy landscapes formed by Y362, N378, and T391 indicate that the binding clefts of C30R and H215Y mutants are larger than the wild-type Tyrp1. In docking simulations, the hydrogen bond and salt bridge interactions that stabilize DHICA in the active site remain similar among Tyrp1, D308N, and R326H. However, the strengths of these interactions and stability of the docked ligand may decrease proportionally to mutation severity due to the larger and less well-defined natures of the binding clefts in mutants. Mutational perturbations in mutants that are not unfolded may result in allosteric alterations to the active site, reducing the stability of protein-ligand interactions.https://www.mdpi.com/1422-0067/22/19/10203melanogenesisTyrp1OCA3disease-related mutant variantsmolecular modeling |
| spellingShingle | Milan H. Patel Monika B. Dolinska Yuri V. Sergeev Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand Binding International Journal of Molecular Sciences melanogenesis Tyrp1 OCA3 disease-related mutant variants molecular modeling |
| title | Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand Binding |
| title_full | Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand Binding |
| title_fullStr | Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand Binding |
| title_full_unstemmed | Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand Binding |
| title_short | Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand Binding |
| title_sort | tyrp1 mutant variants associated with oca3 computational characterization of protein stability and ligand binding |
| topic | melanogenesis Tyrp1 OCA3 disease-related mutant variants molecular modeling |
| url | https://www.mdpi.com/1422-0067/22/19/10203 |
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