Molecular dynamics simulations involving different β-propeller mutations reported in Swiss and French patients correlate with their disease phenotypes

Abstract

Integrin αIIbβ3 is the predominant receptor for fibrinogen which mediates platelet aggregation, an important step in hemostasis and thrombosis. Several mutations have been reported in the genes encoding αIIb and β3 subunits among patients with Glanzmann thrombasthenia, of which 177 are in the β-propeller domain. The two subunits form a heterodimer at the interface between β-propeller and β-I domains of αIIb and β3, respectively with their stability critical for intracellular trafficking, surface expression, and ligand binding. Our study was aimed at retrieving the β-propeller mutations from various databases and studying structural variations due to select mutations upon interaction with fibrinogen using molecular docking and molecular dynamics. Mutations were studied for their impact on phenotypic severity, structural stability, and evolutionary conservation. Molecular docking analysis and molecular dynamics simulations were carried out for αIIb-β3 complexes as well as αIIbβ3-fibrinogen complexes; in particular, E355K structure had more deviations, fluctuations, and other changes which compromised its structural stability and binding affinity when compared to both wild-type and G401C structures. Our comprehensive in silico analysis clearly reiterates that mutations in the β-propeller are not only responsible for structural changes in this domain but also have implications on the overall structure and function of integrin αIIbβ3.

Keywords: Glanzmann Thrombasthenia; Missense mutations; Molecular docking; Molecular dynamics; Β-propeller; αIIbβ3.

Figure 1

Depiction of fibrinogen (γC peptide) interacting domains of αIIbβ3.

Figure 2

Evolutionary conservation analysis of the αIIb amino acid sequence (A) with the highly conserved amino acid residues depicted on the β-propeller structure (B).

Figure 3

Three dimensional interactions of αIIbβ3 complexes after docking with fibrinogen. Wild-type (A), E355K (B), and G401C (C). Chains A and B represent aIIb and b3 subunits, respectively.

Figure 4

RMSD and RMSF plots of wild-type, E355K, and G401C αIIbβ3 structures bound to fibrinogen following MD simulations (500 ns). (A) RMSD values corresponding to the fibrinogen-bound wild-type, E355K, and G401C αIIbβ3 complexes. The x-axis represents time in ns, while the y-axis represents RMSD values in nm. (B) Graphical representation of RMSF values corresponding to the fibrinogen-bound wild-type, E355K, and G401C αIIbβ3 complexes. The x-axis indicates amino acid residues, while the y-axis indicates RMSF values in nm.

Figure 5

Rg and SASA plots of wild-type, E355K, and G401C αIIbβ3 structures bound to fibrinogen following MD simulations (500 ns). (A) Rg values corresponding to the fibrinogen-bound wild-type, E355K, and G401C αIIbβ3 complexes. The x-axis represents time in ns, while the y-axis represents Rg values in nm. (B) SASA values corresponding to the fibrinogen-bound wild-type, E355K, and G401C αIIbβ3 complexes. The x-axis indicates time in ns, while the y-axis indicates area in nm².

Figure 6

KDE plots of Rg and SASA are represented together as collective variables for fibrinogen-bound wild-type (A), E355K (B), and G401C (C) αIIbβ3 complexes.

Figure 7

Graphical representations of H-bond interactions of wild-type, E355K, and G401C αIIbβ3 structures bound to fibrinogen following MD simulations (500 ns). The x-axis represents time in ns, while the y-axis represents number of H-bonds.