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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 partially-extended conformation.A. Snapshots of the U1 free MD 1 at indicated times showing rebending from a partially-extended integrin (colored) to the equilibrated bent conformation (gray). B. Time courses of Cα RMSDs relative to the equilibrated bent structure (red and blue, left ordinate) and head-tail extensions (magenta and cyan, right ordinate) in the U1 free MD 1 (red and magenta) and 2 (blue and cyan). C. Distances between the interacting residues, the nonpolar group (red and magenta) and the Asp393-Arg633 salt bridge (blue and cyan) at the respective hybrid/βTD and hybrid/EGF4 interfaces vs. simulation time of the U1 free MD 1 (red and blue) and 2 (magenta and cyan). As references, the upper and lower dashed lines indicate the respective distances of the nonpolar group and the Asp393-Arg633 salt bridge for the equilibrated bent U1 structure.
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pcbi-1001086-g007: Free MD simulations of a partially-extended conformation.A. Snapshots of the U1 free MD 1 at indicated times showing rebending from a partially-extended integrin (colored) to the equilibrated bent conformation (gray). B. Time courses of Cα RMSDs relative to the equilibrated bent structure (red and blue, left ordinate) and head-tail extensions (magenta and cyan, right ordinate) in the U1 free MD 1 (red and magenta) and 2 (blue and cyan). C. Distances between the interacting residues, the nonpolar group (red and magenta) and the Asp393-Arg633 salt bridge (blue and cyan) at the respective hybrid/βTD and hybrid/EGF4 interfaces vs. simulation time of the U1 free MD 1 (red and blue) and 2 (magenta and cyan). As references, the upper and lower dashed lines indicate the respective distances of the nonpolar group and the Asp393-Arg633 salt bridge for the equilibrated bent U1 structure.

Mentions: We performed two sets of free dynamics to examine the stabilities of integrin conformations along the unbending pathway after overcoming the major barrier. The first set studied a partially-extended conformation obtained right after the major force peak. Two structures from the respective trajectories of the U1 SMD 1 and U2 SMD 2 at ∼5 nm extensions were selected as starting structures for free MD 1 & 2, respectively (Fig. 2F). In the free MD simulations, the force at the βA domain was turned off. The constraint at the βTD was released in the free MD 1 but maintained in the free MD 2. In both simulations, the integrin gradually bent back (Fig. 7A and Video S3) as indicated by the decreased Cα RMSD relative to the equilibrated bent conformation and the reduced head-tail extension (Fig. 7B). This is particularly evident in the free MD 1 where the Cα RMSD dropped to ∼4 Å within 21 ns and the integrin returned nearly completely to its bent conformation. Not only did the overall structure bend back, but some important interactions between the headpiece and tailpiece that were broken during the simulated unbending were also recovered. Two groups of interactions, including the polar interactions between the hybrid domain and βTD and the nonpolar interactions between the hybrid and EGF4 domains, were gauged by the respective distances between the center of mass (COM) of the two sidechain oxygen atoms of Asp393 and the COM of the three sidechain nitrogen atoms of Arg633 and between the COM of the sidechains of Leu375, Ile380, and Leu383 and the COM of the sidechains of Met568, Leu573, and Leu574. These two distances were reduced when the integrin bent back (Fig. 7C). In free MD 1, the distance of the nonpolar interactions suddenly dropped to ∼4 Å and persisted to the end of the simulation, indicating that the nonpolar interactions between the hybrid and EGF4 domains were recovered. These results demonstrated again the importance of the nonpolar interactions in stabilizing the bent conformation. By comparison, the polar interactions were not recovered in the simulations because the Asp393-Arg633 distance was still much larger than that in the bent integrin (Fig. 7C).


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 partially-extended conformation.A. Snapshots of the U1 free MD 1 at indicated times showing rebending from a partially-extended integrin (colored) to the equilibrated bent conformation (gray). B. Time courses of Cα RMSDs relative to the equilibrated bent structure (red and blue, left ordinate) and head-tail extensions (magenta and cyan, right ordinate) in the U1 free MD 1 (red and magenta) and 2 (blue and cyan). C. Distances between the interacting residues, the nonpolar group (red and magenta) and the Asp393-Arg633 salt bridge (blue and cyan) at the respective hybrid/βTD and hybrid/EGF4 interfaces vs. simulation time of the U1 free MD 1 (red and blue) and 2 (magenta and cyan). As references, the upper and lower dashed lines indicate the respective distances of the nonpolar group and the Asp393-Arg633 salt bridge for the equilibrated bent U1 structure.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1001086-g007: Free MD simulations of a partially-extended conformation.A. Snapshots of the U1 free MD 1 at indicated times showing rebending from a partially-extended integrin (colored) to the equilibrated bent conformation (gray). B. Time courses of Cα RMSDs relative to the equilibrated bent structure (red and blue, left ordinate) and head-tail extensions (magenta and cyan, right ordinate) in the U1 free MD 1 (red and magenta) and 2 (blue and cyan). C. Distances between the interacting residues, the nonpolar group (red and magenta) and the Asp393-Arg633 salt bridge (blue and cyan) at the respective hybrid/βTD and hybrid/EGF4 interfaces vs. simulation time of the U1 free MD 1 (red and blue) and 2 (magenta and cyan). As references, the upper and lower dashed lines indicate the respective distances of the nonpolar group and the Asp393-Arg633 salt bridge for the equilibrated bent U1 structure.
Mentions: We performed two sets of free dynamics to examine the stabilities of integrin conformations along the unbending pathway after overcoming the major barrier. The first set studied a partially-extended conformation obtained right after the major force peak. Two structures from the respective trajectories of the U1 SMD 1 and U2 SMD 2 at ∼5 nm extensions were selected as starting structures for free MD 1 & 2, respectively (Fig. 2F). In the free MD simulations, the force at the βA domain was turned off. The constraint at the βTD was released in the free MD 1 but maintained in the free MD 2. In both simulations, the integrin gradually bent back (Fig. 7A and Video S3) as indicated by the decreased Cα RMSD relative to the equilibrated bent conformation and the reduced head-tail extension (Fig. 7B). This is particularly evident in the free MD 1 where the Cα RMSD dropped to ∼4 Å within 21 ns and the integrin returned nearly completely to its bent conformation. Not only did the overall structure bend back, but some important interactions between the headpiece and tailpiece that were broken during the simulated unbending were also recovered. Two groups of interactions, including the polar interactions between the hybrid domain and βTD and the nonpolar interactions between the hybrid and EGF4 domains, were gauged by the respective distances between the center of mass (COM) of the two sidechain oxygen atoms of Asp393 and the COM of the three sidechain nitrogen atoms of Arg633 and between the COM of the sidechains of Leu375, Ile380, and Leu383 and the COM of the sidechains of Met568, Leu573, and Leu574. These two distances were reduced when the integrin bent back (Fig. 7C). In free MD 1, the distance of the nonpolar interactions suddenly dropped to ∼4 Å and persisted to the end of the simulation, indicating that the nonpolar interactions between the hybrid and EGF4 domains were recovered. These results demonstrated again the importance of the nonpolar interactions in stabilizing the bent conformation. By comparison, the polar interactions were not recovered in the simulations because the Asp393-Arg633 distance was still much larger than that in the bent integrin (Fig. 7C).

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