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Molecular dynamics simulations of forced unbending of integrin α(v)β₃.

Chen W, Lou J, Hsin J, Schulten K, Harvey SC, Zhu C - PLoS Comput. Biol. (2011)

Bottom Line: By comparison, a fully-extended conformation was stable.A newly-formed coordination between the α(v) Asp457 and the α-genu metal ion might contribute to the stability of the fully-extended conformation.These results reveal the dynamic processes and pathways of integrin conformational changes with atomic details and provide new insights into the structural mechanisms of integrin activation.

View Article: PubMed Central - PubMed

Affiliation: Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America.

ABSTRACT
Integrins may undergo large conformational changes during activation, but the dynamic processes and pathways remain poorly understood. We used molecular dynamics to simulate forced unbending of a complete integrin α(v)β₃ ectodomain in both unliganded and liganded forms. Pulling the head of the integrin readily induced changes in the integrin from a bent to an extended conformation. Pulling at a cyclic RGD ligand bound to the integrin head also extended the integrin, suggesting that force can activate integrins. Interactions at the interfaces between the hybrid and β tail domains and between the hybrid and epidermal growth factor 4 domains formed the major energy barrier along the unbending pathway, which could be overcome spontaneously in ~1 µs to yield a partially-extended conformation that tended to rebend. By comparison, a fully-extended conformation was stable. A newly-formed coordination between the α(v) Asp457 and the α-genu metal ion might contribute to the stability of the fully-extended conformation. These results reveal the dynamic processes and pathways of integrin conformational changes with atomic details and provide new insights into the structural mechanisms of integrin activation.

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Free MD simulations of a fully-extended conformation.A. Snapshots of the U1 free MD 3 at indicated times showing the relaxation of a fully-extended integrin. Dashed boxes indicated the location of the α-knee Ca2+. B. Time courses of Cα RMSDs relative to the equilibrated bent structure (red and blue) or the starting fully-extended structure (magenta and cyan) in the U1 free MD 3 (red and magenta) and 4 (blue and cyan). C & D. Metal-ion coordination at the α-knee of the extended U1 at the end of the free MD 3 (C) or the bent U1 at the end of equilibration (D). Sticks represent residues and the red sphere represents the α-knee Ca2+. E. Time courses of distances between Asp457 of the αV subunit and the α-knee Ca2+ in the U1 free MD 3 (red), the U1 free MD 4 (blue), and the equilibration of the bent U1 (magenta).
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pcbi-1001086-g008: Free MD simulations of a fully-extended conformation.A. Snapshots of the U1 free MD 3 at indicated times showing the relaxation of a fully-extended integrin. Dashed boxes indicated the location of the α-knee Ca2+. B. Time courses of Cα RMSDs relative to the equilibrated bent structure (red and blue) or the starting fully-extended structure (magenta and cyan) in the U1 free MD 3 (red and magenta) and 4 (blue and cyan). C & D. Metal-ion coordination at the α-knee of the extended U1 at the end of the free MD 3 (C) or the bent U1 at the end of equilibration (D). Sticks represent residues and the red sphere represents the α-knee Ca2+. E. Time courses of distances between Asp457 of the αV subunit and the α-knee Ca2+ in the U1 free MD 3 (red), the U1 free MD 4 (blue), and the equilibration of the bent U1 (magenta).

Mentions: The second set of stability analyses was performed on a fully-extended conformation. Two simulations, free MD 3 & 4, were run with their starting structures selected from the trajectories of the U1 SMD 1 & 2, respectively, at ∼16 nm extensions (Fig. 2F). Free MD began after turning off the pulling force on the βA domain. The constraint at the βTD was released in the free MD 3 but maintained in the free MD 4. In both simulations, the integrin was relaxed and slightly bent back, but remained in a globally extended conformation for >20 ns (Fig. 8A and Video S4). Both Cα RMSDs measured from the equilibrated bent conformation and from the starting extended conformation reached plateaus after ∼5 ns (Fig. 8B). Interestingly, in both simulations, Asp457 of the thigh domain moved to coordinate with the Ca2+ ion at the genu of the αV subunit (Fig. 8C), as observed by a sudden drop in the distance between the COM of the two Asp457 sidechain oxygens and this Ca2+ ion to <4 Å at ∼3 or ∼18 ns, respectively, which persisted throughout the remaining simulations (Fig. 8E), indicating the stability of the new coordination once it was formed. It should be noted that in the bent conformation, Asp457 was too far away (∼14 Å) to coordinate with the αV-genu Ca2+ (Fig. 8D). Only after integrin extension was it physically possible to interact with the αV-genu Ca2+. These results suggest a role for this newly-formed coordination involving Asp457 in stabilizing the extended conformation.


Molecular dynamics simulations of forced unbending of integrin α(v)β₃.

Chen W, Lou J, Hsin J, Schulten K, Harvey SC, Zhu C - PLoS Comput. Biol. (2011)

Free MD simulations of a fully-extended conformation.A. Snapshots of the U1 free MD 3 at indicated times showing the relaxation of a fully-extended integrin. Dashed boxes indicated the location of the α-knee Ca2+. B. Time courses of Cα RMSDs relative to the equilibrated bent structure (red and blue) or the starting fully-extended structure (magenta and cyan) in the U1 free MD 3 (red and magenta) and 4 (blue and cyan). C & D. Metal-ion coordination at the α-knee of the extended U1 at the end of the free MD 3 (C) or the bent U1 at the end of equilibration (D). Sticks represent residues and the red sphere represents the α-knee Ca2+. E. Time courses of distances between Asp457 of the αV subunit and the α-knee Ca2+ in the U1 free MD 3 (red), the U1 free MD 4 (blue), and the equilibration of the bent U1 (magenta).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3040657&req=5

pcbi-1001086-g008: Free MD simulations of a fully-extended conformation.A. Snapshots of the U1 free MD 3 at indicated times showing the relaxation of a fully-extended integrin. Dashed boxes indicated the location of the α-knee Ca2+. B. Time courses of Cα RMSDs relative to the equilibrated bent structure (red and blue) or the starting fully-extended structure (magenta and cyan) in the U1 free MD 3 (red and magenta) and 4 (blue and cyan). C & D. Metal-ion coordination at the α-knee of the extended U1 at the end of the free MD 3 (C) or the bent U1 at the end of equilibration (D). Sticks represent residues and the red sphere represents the α-knee Ca2+. E. Time courses of distances between Asp457 of the αV subunit and the α-knee Ca2+ in the U1 free MD 3 (red), the U1 free MD 4 (blue), and the equilibration of the bent U1 (magenta).
Mentions: The second set of stability analyses was performed on a fully-extended conformation. Two simulations, free MD 3 & 4, were run with their starting structures selected from the trajectories of the U1 SMD 1 & 2, respectively, at ∼16 nm extensions (Fig. 2F). Free MD began after turning off the pulling force on the βA domain. The constraint at the βTD was released in the free MD 3 but maintained in the free MD 4. In both simulations, the integrin was relaxed and slightly bent back, but remained in a globally extended conformation for >20 ns (Fig. 8A and Video S4). Both Cα RMSDs measured from the equilibrated bent conformation and from the starting extended conformation reached plateaus after ∼5 ns (Fig. 8B). Interestingly, in both simulations, Asp457 of the thigh domain moved to coordinate with the Ca2+ ion at the genu of the αV subunit (Fig. 8C), as observed by a sudden drop in the distance between the COM of the two Asp457 sidechain oxygens and this Ca2+ ion to <4 Å at ∼3 or ∼18 ns, respectively, which persisted throughout the remaining simulations (Fig. 8E), indicating the stability of the new coordination once it was formed. It should be noted that in the bent conformation, Asp457 was too far away (∼14 Å) to coordinate with the αV-genu Ca2+ (Fig. 8D). Only after integrin extension was it physically possible to interact with the αV-genu Ca2+. These results suggest a role for this newly-formed coordination involving Asp457 in stabilizing the extended conformation.

Bottom Line: By comparison, a fully-extended conformation was stable.A newly-formed coordination between the α(v) Asp457 and the α-genu metal ion might contribute to the stability of the fully-extended conformation.These results reveal the dynamic processes and pathways of integrin conformational changes with atomic details and provide new insights into the structural mechanisms of integrin activation.

View Article: PubMed Central - PubMed

Affiliation: Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America.

ABSTRACT
Integrins may undergo large conformational changes during activation, but the dynamic processes and pathways remain poorly understood. We used molecular dynamics to simulate forced unbending of a complete integrin α(v)β₃ ectodomain in both unliganded and liganded forms. Pulling the head of the integrin readily induced changes in the integrin from a bent to an extended conformation. Pulling at a cyclic RGD ligand bound to the integrin head also extended the integrin, suggesting that force can activate integrins. Interactions at the interfaces between the hybrid and β tail domains and between the hybrid and epidermal growth factor 4 domains formed the major energy barrier along the unbending pathway, which could be overcome spontaneously in ~1 µs to yield a partially-extended conformation that tended to rebend. By comparison, a fully-extended conformation was stable. A newly-formed coordination between the α(v) Asp457 and the α-genu metal ion might contribute to the stability of the fully-extended conformation. These results reveal the dynamic processes and pathways of integrin conformational changes with atomic details and provide new insights into the structural mechanisms of integrin activation.

Show MeSH