Fig 1.
Tridimensional structure and schematic representation of PFN1.
The PLP binding domain and the actin-binding domain of PFN1 are represented in blue and green, respectively. The mutation sites: C71, M114, E117 and G118, are represented in red. The dark yellow arrow shows the residue threonine 89. (A) Tridimensional structure of PFN1 (PDB ID: 1PFL). (B) Schematic representation of PFN1.
Fig 2.
Functional prediction results of each PFN1 nsSNV.
The four known nsSNVs of PFN1 were analyzed using eight different functional prediction algorithms. The bar plot indicates the number of neutral and deleterious predictions of each PFN1 nsSNV, according to the used algorithms. Blue bars indicate neutral predictions while red bars indicate the number of deleterious predictions.
Table 1.
Functional prediction analysis of PFN1 natural variants.
Fig 3.
Evolutionary conservation analysis of PFN1.
The PFN1 conservation profile shown in three different angles. Each PFN1 amino acid is represented as a space-filling model and colored according to its conservation score. The ConSurf coloring scheme is shown in the color-coding bar. According to ConSurf, the positions 71, 114 and 118 are highly conserved, while the position 117 is average conserved.
Fig 4.
Backbone RMSD of the wild-type PFN1 and its natural variants.
The RMSD for the backbone atoms of the wild-type structure and variants at 300K shown as a function of time. The wild type is represented in black,variant C71G is represented in red, variant M114T is represented in blue, variant E117G is represented in green, and variant G118V is represented in purple.
Fig 5.
RMSF of the wild-type PFN1 and its natural variants.
The RMSF of each residue of the PFN1 wild-type and variants at 300K is shown. Schematic representations of PFN1 domains and secondary structure are shown to further comparison. The PLP binding domain and actin-binding domains of PFN1 are represented in blue and green, respectively. The PFN1 mutation sites are colored red. Alpha-helices are represented by magenta arrows, beta-strands are represented by yellow barrels, and the coils are represented by the thin black lines. The dark yellow line shows the residue threonine 89. (A) The wild type is represented in black and variant C71G is represented in red. (B) The wild type is represented in black and variant M114T is represented in blue. (C) The wild type is represented in black and variant E117G is represented in green. (D) The wild type is represented in black and variant G118V is represented in purple.
Fig 6.
The B-factor representation of PFN1 wild-type and its natural variants.
The B-factor for each residue of the PFN1 wild-type and variants represented in a coloring-thickness scheme. Red and bulky structures represent high values and dark blue and thin structures represent low values. (A) B-factor representation of the wild type PFN1. (B) B-factor representation of the C71G variant. (C) B-factor representation of the M114T variant. (D) B-factor representation of the E117G variant. (E) B-factor representation of the G118V variant. (F) Schematic representation of PFN1 structure to further comparison. The PLP binding domain and actin-binding domains of PFN1 are represented in blue and green, respectively. The PFN1 mutation sites are colored red. The dark yellow arrow shows the residue threonine 89.
Fig 7.
The radius of gyration (Rg) of the wild-type PFN1 and its natural variants.
The Rg for the Cα atoms of the wild-type PFN1 and its natural variants at 300 K are shown as a function of time. (A) The wild type is represented in black and variant C71G is represented in red. (B) The wild type is represented in black and variant M114T is represented in blue. (C) The wild type is represented in black and variant E117G is represented in green. (D) The wild type is represented in black and variant G118V is represented in purple.
Fig 8.
Intramolecular hydrogen bonds (Hb) for the wild-type PFN1 and its natural variants.
The number of intramolecular Hb formed at 300 K throughout the simulations is shown as a function of time. (A) The wild-type is represented in black and variant C71G is represented in red. (B) The wild type is represented in black and variant M114T is represented in blue. (C) The wild type is represented in black and variant E117G is represented in green. (D) The wild type is represented in black and variant G118V is represented in purple.
Fig 9.
Schematic representation of the PFN1 mechanism of action and how it can be disrupted by missense mutations.
PFN1 is represented in green, actin monomer is represented in blue, Ena/VASP is represented in orange, and the actin polymer is represented by the blue chained filament. Black arrows indicate the normal PFN1 mechanism of action, while the inhibitory arrow (red) indicates how this mechanism could be disrupted by missense mutations. i) The unbound PFN1 is able to interact with actin monomers. ii) PFN1 interacts through its actin-binding domain with an actin monomer. iii) Upon binding to the actin monomer, PFN1 interacts through its PLP-binding domain with Enabled/vasodilator-stimulated phosphoproteins (Ena/VASP). iv) Ena/VASP, in turn, is responsible for adding the actin monomer captured by PFN1 to the crescent actin filament polymer. v) After the delivery of actin monomer, the PFN1 is released from Ena/VASP. The C71G, M114T, E117G and G118V missense mutations in PFN1 are known to affect the actin, and PLP-binding of BDNF. We proposed that it may occur due to the flexibility alterations at the actin and PLP-binding domains and adjacent residues of PFN1.