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Conformational Selection and Induced Fit Mechanisms in the Binding of an Anticancer Drug to the c-Src Kinase.

Morando MA, Saladino G, D'Amelio N, Pucheta-Martinez E, Lovera S, Lelli M, López-Méndez B, Marenchino M, Campos-Olivas R, Gervasio FL - Sci Rep (2016)

Bottom Line: The conserved three amino-acid DFG motif undergoes an "in to out" movement resulting in a particular inactive conformation to which "type II" kinase inhibitors, such as the anti-cancer drug Imatinib, bind.Here we combine various NMR experiments and surface plasmon resonance with enhanced sampling molecular dynamics simulations to shed light into the conformational dynamics associated with the binding of Imatinib to the proto-oncogene c-Src.Moreover, an external binding pose and local unfolding (cracking) of the aG helix are observed.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fernandez Almagro 3, 28029, Madrid, Spain.

ABSTRACT
Understanding the conformational changes associated with the binding of small ligands to their biological targets is a fascinating and meaningful question in chemistry, biology and drug discovery. One of the most studied and important is the so-called "DFG-flip" of tyrosine kinases. The conserved three amino-acid DFG motif undergoes an "in to out" movement resulting in a particular inactive conformation to which "type II" kinase inhibitors, such as the anti-cancer drug Imatinib, bind. Despite many studies, the details of this prototypical conformational change are still debated. Here we combine various NMR experiments and surface plasmon resonance with enhanced sampling molecular dynamics simulations to shed light into the conformational dynamics associated with the binding of Imatinib to the proto-oncogene c-Src. We find that both conformational selection and induced fit play a role in the binding mechanism, reconciling opposing views held in the literature. Moreover, an external binding pose and local unfolding (cracking) of the aG helix are observed.

No MeSH data available.


Difference of combined 1H, 15N chemical shift Δδ for Src upon binding of Imatinib (left) and Dasatinib (right).Ligands are shown as blue sticks. Residues for which data is not available are shown in dark grey.
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f3: Difference of combined 1H, 15N chemical shift Δδ for Src upon binding of Imatinib (left) and Dasatinib (right).Ligands are shown as blue sticks. Residues for which data is not available are shown in dark grey.

Mentions: The changes in chemical shifts due to the binding of Imatinib are reported in Fig. 3 and SI Fig. S6. The residues that become visible only in the bound-form are shown in Fig. S6 and include many residues of the αC and αG helices as well as the regions closest to Imatinib of αE, αF and αI. The appearance of signals from the αC helix and from two flanking beta strands, indicating a significant change in their conformational dynamics, is of particular interest. This helix is known to reposition in the bound form (αC-in) through the formation of a salt bridge between Glu310 and Lys29535. The αC helix appears to be essential in modulating the function of the protein and its movement is connected with the conformational changes of the activation loop36.


Conformational Selection and Induced Fit Mechanisms in the Binding of an Anticancer Drug to the c-Src Kinase.

Morando MA, Saladino G, D'Amelio N, Pucheta-Martinez E, Lovera S, Lelli M, López-Méndez B, Marenchino M, Campos-Olivas R, Gervasio FL - Sci Rep (2016)

Difference of combined 1H, 15N chemical shift Δδ for Src upon binding of Imatinib (left) and Dasatinib (right).Ligands are shown as blue sticks. Residues for which data is not available are shown in dark grey.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4834493&req=5

f3: Difference of combined 1H, 15N chemical shift Δδ for Src upon binding of Imatinib (left) and Dasatinib (right).Ligands are shown as blue sticks. Residues for which data is not available are shown in dark grey.
Mentions: The changes in chemical shifts due to the binding of Imatinib are reported in Fig. 3 and SI Fig. S6. The residues that become visible only in the bound-form are shown in Fig. S6 and include many residues of the αC and αG helices as well as the regions closest to Imatinib of αE, αF and αI. The appearance of signals from the αC helix and from two flanking beta strands, indicating a significant change in their conformational dynamics, is of particular interest. This helix is known to reposition in the bound form (αC-in) through the formation of a salt bridge between Glu310 and Lys29535. The αC helix appears to be essential in modulating the function of the protein and its movement is connected with the conformational changes of the activation loop36.

Bottom Line: The conserved three amino-acid DFG motif undergoes an "in to out" movement resulting in a particular inactive conformation to which "type II" kinase inhibitors, such as the anti-cancer drug Imatinib, bind.Here we combine various NMR experiments and surface plasmon resonance with enhanced sampling molecular dynamics simulations to shed light into the conformational dynamics associated with the binding of Imatinib to the proto-oncogene c-Src.Moreover, an external binding pose and local unfolding (cracking) of the aG helix are observed.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), c/Melchor Fernandez Almagro 3, 28029, Madrid, Spain.

ABSTRACT
Understanding the conformational changes associated with the binding of small ligands to their biological targets is a fascinating and meaningful question in chemistry, biology and drug discovery. One of the most studied and important is the so-called "DFG-flip" of tyrosine kinases. The conserved three amino-acid DFG motif undergoes an "in to out" movement resulting in a particular inactive conformation to which "type II" kinase inhibitors, such as the anti-cancer drug Imatinib, bind. Despite many studies, the details of this prototypical conformational change are still debated. Here we combine various NMR experiments and surface plasmon resonance with enhanced sampling molecular dynamics simulations to shed light into the conformational dynamics associated with the binding of Imatinib to the proto-oncogene c-Src. We find that both conformational selection and induced fit play a role in the binding mechanism, reconciling opposing views held in the literature. Moreover, an external binding pose and local unfolding (cracking) of the aG helix are observed.

No MeSH data available.