Fig 1.
Crystallographic structure and schematic representation of TPH2.
The regulatory, catalytic and oligomerization domains of TPH2 are represented in yellow, blue and pink, respectively. (A) Secondary structure representation of the crystallographic structure of TPH2 (PDB ID: 4V06). The protein surface is also shown. (B) Schematic representation of TPH2. The region corresponding to the experimentally determined structure of TPH2 is indicated by the bracket.
Fig 2.
Functional prediction of TPH2 mutations.
The 46 known TPH2 mutations were analyzed using eight different functional prediction algorithms. The bar plot indicates the number of neutral (gray bars) and deleterious (red bars) predictions for each TPH2 mutation.
Fig 3.
Evolutionary conservation analysis of TPH2 protein.
(A) The evolutionary conservation profile of the TPH2 protein is shown at three different angles. Each amino acid of TPH2 is represented as a space-filling model and colored according to its ConSurf conservation score. The color-coding bar shows the ConSurf coloring scheme, which varies from cyan and highly variable to maroon and highly conserved. The conservation score for each amino acid of TPH2 affected by deleterious mutations, i.e., P206S, R303W, and R441H, are also shown. (B) The bar plot shows the ConSurf score for each amino acid of TPH2 affected by mutations. The bar plot was colored according to the ConSurf coloring scheme.
Fig 4.
Backbone RMSD of WT TPH2 and its variants.
The RMSD for the backbone atoms of TPH2 WT and variants at 300 K is shown as a function of time. WT is represented in black, variant P206S is represented in dark yellow, variant R303W is represented in purple, and variant R441H is represented in turquoise.
Fig 5.
RMSF per residue of WT TPH2 and its variants.
The RMSF of each residue of TPH2 WT and variants at 300 K is shown as a line plot. (A) Comparison between the WT (black) and variant P206S (dark yellow). (B) Comparison between the WT (black) and variant R303W (purple). (C) Comparison between the WT (black) and variant R441H (turquoise).
Fig 6.
B-factor per residue of WT TPH2 and its variants.
Each residue of TPH WT (A) and variants P206S (B), R303W (C), and R441H (D) is colored and sized according to its B-factor. The coloring-thickness scale varies from dark blue and thin (highly rigid residues) to red and thick (highly flexible residues).
Fig 7.
PCA of WT TPH2 and its variants.
Projection of the first two principal components (PC1 and PC2) extracted from the essential dynamics. (A) PCA comparison between WT TPH2 (black) and its variant P206S (dark yellow). (B) PCA comparison between WT TPH2 (black) and its variant R303W (purple). (C) PCA comparison between WT TPH2 (black) and its variant R441H (turquoise). (D) Superimposed PCA comparison between WT TPH (black) and its variants P206S (dark yellow), R303W (purple), and R441H (turquoise).
Fig 8.
RMSF contribution to PC1 of WT TPH2 and its variants.
The RMSF contribution of each protein residue to PC1 is shown as a line plot and projected on the corresponding structure. Each residue of TPH2 WT and variants was colored and sized according to its RMSF contribution. The coloring-thickness scale varies from dark blue and thin (low fluctuations) to red and thick (high fluctuations). (A) RMSF contribution of WT TPH2 to PC1. (B) RMSF contribution of variant P206S to PC1. (C) RMSF contribution of variant R303W to PC1. (D) RMSF contribution of variant R441H to PC1.
Fig 9.
RMSF contribution to PC2 of WT TPH2 and its variants.
The RMSF contribution of each protein residue to PC2 is shown as a line plot and projected on the corresponding structure. Each residue of TPH2 WT and variants was colored and sized according to its RMSF contribution. The coloring-thickness scale varies from dark blue and thin (low fluctuations) to red and thick (high fluctuations). (A) RMSF contribution of WT TPH2 to PC2. (B) RMSF contribution of variant P206S to PC2. (C) RMSF contribution of variant R303W to PC2. (D) RMSF contribution of variant R441H to PC2.
Fig 10.
Secondary structure analysis of TPH2 WT and its variants.
The average number (in percentages) of alpha-helices, beta-sheets and coils formed throughout the simulations of WT TPH2 and its variants P206S, R303W, and R441H are shown as a bar plot. The error bar represents the standard deviation. The bar plot was designed using the ggplot2 library implemented in R software.
Fig 11.
Hydrogen bond analysis of TPH2 WT and its variants.
The number of hydrogen bonds formed during the simulations of TPH2 WT and its variants is shown as a function of time. (A) Comparison between the WT (black) and P206S variant (dark yellow). (B) Comparison between the WT (black) and R303W variants (purple). (C) Comparison between the WT (black) and R441H variant (turquoise).
Fig 12.
Hydrophobic contact analysis of TPH2 WT and its variants.
The number of hydrophobic contacts formed during the simulations of TPH2 WT and its variants is shown as a function of time. (A) Comparison between the WT (black) and P206S variant (dark yellow). (B) Comparison between the WT (black) and R303W variants (purple). (C) Comparison between the WT (black) and R441H variant (turquoise).
Table 1.
MM-PBSA analysis of WT TPH2 and its variants.