Activation mechanisms of αVβ3 integrin by binding to fibronectin: A computational study

Abstract

Integrin αVβ3 plays an important role in regulating cellular activities and in human diseases. Although the structure of αVβ3 has been studied by crystallography and electron microscopy, the detailed activation mechanism of integrin αVβ3 induced by fibronectin remains unclear. In this study, we investigated the conformational and dynamical motion changes of Mn²⁺ -bound integrin αVβ3 by binding to fibronectin with molecular dynamics simulations. Results showed that fibronectin binding to integrin αVβ3 caused the changes of the conformational flexibility of αVβ3 domains, the essential mode of motion for the domains of αV subunit and β3 subunit and the degrees of correlated motion of residues between the domains of αV subunit and β3 subunit of integrin αVβ3. The angle of Propeller domain with respect to the Calf-2 domain of αV subunit and the angle of Hybrid domain with respect to βA domain of β3 subunit significantly increased when integrin αVβ3 was bound to fibronectin. These changes could result in the conformational change tendency of αVβ3 from a bend conformation to an extended conformation and lead to the open swing of Hybrid domain relative to βA domain of β3 subunit, which have demonstrated their importance for αVβ3 activation. Fibronectin binding to integrin αVβ3 significantly decreased the relative position of α1 helix to βA domain and that to metal ion-dependent adhesion site, stabilized Mn²⁺ ions binding in integrin αVβ3 and changed fibronectin conformation, which are important for αVβ3 activation. Results from this study provide important molecular insight into the "outside-in" activation mechanism of integrin αVβ3 by binding to fibronectin.

Keywords: activation mechanism; conformational and dynamical motion changes; fibronectin; integrin αVβ3; molecular dynamics simulation.

Figure 1

Modeled structure of integrin αVβ3. Left figure is for αV subunit and right figure for β3 subunit. The Propeller, Thigh, Calf‐1 and Calf‐2 domains of αV shown in blue, cyan, gray and light blue, respectively. The PSI, Hybrid, βA, EGF, and βTD domains of β3 e shown in yellow, orange, red, purple, and green, respectively.

Figure 2

The root mean squared fluctuation (RMSF) comparison of αV and β3 subunit of integrin αVβ3 with and without bound to fibronectin (red line: integrin αVβ3 bound with fibronectin; black line: integrin αVβ3 without bound to fibronectin). (A) RMSF of αV subunit comparison; (B) RMSF of β3 subunit comparison.

Figure 3

(A) Comparison of the angle of Propeller domain with respect to the Calf‐2 domain of αV subunit of integrin αVβ3 with and without bound to fibronectin. Left figure shows the definition of the angle of Propeller domain with respect to the Calf‐2 domain with genu site as the pivot (each domain represented by its center of mass (COM)). (B) Comparison of the angle of Hybrid domain with respect to βA domain of β3 subunit of integrin αVβ3 with and without bound to fibronectin. Left figure shows the definition of the angle of Hybrid domain with respect to βA domain with residue 1074 between Hybrid domain and βA domain as pivot (each domain represented by its COM). Hybrid domain (in cyan) in αVβ3 without bound to fibronectin is superposed with that in αVβ3 bound to fibronectin, βA domain in αVβ3 without bound to fibronectin is shown in blue and βA in αVβ3 bound to fibronectin is shown in red.

Figure 4

(A) Distance between COM of βA domain and α1 helix, (B) Distance between COM of α1 helix and metal ion dependent adhesion site (MIDAS).

Figure 5

Principal dynamic modes for integrin αVβ3 without bound to fibronectin (A) and bound with fibronectin (B) from principle component analyses. The αV subunit shown in blue, β3 subunit shown in red and porcupines showing the dynamic modes shown in green. The images were made with VMD program.

Figure 6

Dynamical cross‐correlation maps to compare the degree of correlated motion of the residues in αV and β3 subunit of integrin αVβ3 bound with fibronectin (bottom‐right) and without bound to fibronectin (top‐left).

Figure 7

Coordination of Mn²⁺ ions at metal binding sites in integrin αVβ3 without bound to fibronectin (A) and bound with fibronectin (B). Mn²⁺ ion at MIDAS shown in green, Mn²⁺ ion at LIBMS shown in red, and Mn²⁺ ion at ADMIDAS shown in blue. (C) Distance between Mn²⁺ ion at MIDAS and at ADMIDAS. (D) Distance between Mn²⁺ ion at MIDAS and at LIBMS. (E) Distance between Mn²⁺ ion at ADMIDAS and at LIBMS.

Figure 8

Conformational change of fibronectin. (A) Schematic representation of the angle between FnIII9 and FnIII10 with and without bound to αVβ3. The angle is formed by COM of FnIII9, pivot (residue 1448 of Fn), and COM of FnIII10. αV subunit shown in blue, β3 subunit in red, free Fn in black and Fn in liganded‐αVβ3 shown in yellow. The SDL in βA domain of β3 subunit is in purple. Mn²⁺ ion at MIDAS shown in green, Mn²⁺ ion at LIBMS shown in red, and Mn²⁺ ion at ADMIDAS shown in blue. FnIII10 are superposed with and without bound to integrin.) (B) Change of the angle between FnIII9 and FnIII10. Left for Fn in liganded‐αVβ3, right for free Fn. (C) Change of distance between RGD loop and synergy site. Left for Fn in liganded‐αVβ3, right for free Fn.