Fig 1.
CDK2 conformational landscape.
A) CDK2 structure in the active conformation (PDB code: 1FIN). Residues used for the calculation of the RMSD distance matrix are color coded: N-lobe β strands (orange), αC-helix (red), DFG and catalytic loop (yellow), and C-lobe helixes D-E-F-I (green). B) Conformational landscape calculated using 255 CDK2 crystal structures. Crystal structures were clustered in: active (red), type A inactive (green), type B inactive (blue), DFG-out (cyan), and open (pink). A representative for each cluster is reported.
Fig 2.
CDK2 crystal structure clusters.
Crystal structures of each cluster superposed to a reference structure. The main structural elements are reported. A) Active (1FIN was used as reference); B) type A inactive (3PXR); C) type B inactive (4GCJ); D) DFG-out (5A14) and E) open (3PXF).
Fig 3.
Apo CDK2 plain MD simulations.
Plain MD simulations were numbered 1 (starting from the active conformation), 2 (from the inactive conformation) and 3 (from the open conformation). A) The distances between the donor-acceptor couples in Glu51-Arg126, Lys33-Glu51, and Arg150-Glu51 are reported for the three simulations B) Samples from these simulations were projected to the cMDS landscape and represented as a scatter plot. Snapshots were colored following the progress of the simulation (see the bars above the scatter plots). Colors run from blue at the beginning of the simulations to dark red at the end of the simulations. C) The same samples analyzed using the RMSD of the A-loop from the inactive conformation and the difference in distances between the couples Glu51-Arg150 and Lys33-Glu51. D) Representation of simulation samples using the RMSD of the A-loop and the RMSD of the αC-helix from the inactive conformation. Samples were colored from dark blue to dark red according to the simulation time.
Fig 4.
apo CDK2 accelerated MD simulations.
A) The αC-helix and A-loop of metastable state representatives (white) and open (green) conformation superposed to the active conformation. B) Free energy landscape represented using the cMDS components. The metastable intermediate states are circled. C) Free energy landscape represented using the RMSD of the A-loop from the inactive conformation and the difference in distances between the couples Glu51-Arg150 and Lys33-Glu51. D) Free energy landscape represented using the RMSD of the A-loop and the RMSD of the αC-helix from the inactive conformation. Energies equal or above 30 kcal/mol from the global minimum were cut and represented in white for the sake of clarity.
Fig 5.
CDK2/ANS complex plain MD simulations.
A) Binding interactions and B) Binding site of ANS1. C) Samples from plain MD were projected to the cMDS landscape and represented as a scatter plot. Snapshots were colored following the progress of the simulation (see the bars above the scatter plots). Colors run from blue at the beginning of the simulations to dark red at the end of the simulations. D) Representation of plain MD simulation samples using the RMSD of the A-loop from the inactive conformation and the difference in distances between the couples Glu51-Arg150 and Lys33-Glu51. E) Representation of plain MD simulation samples using the RMSD of the A-loop and the RMSD of the αC-helix from the inactive conformation.
Fig 6.
CDK2/ANS complex accelerated MD simulations.
A) Representatives of free energy minima (white) superposed to the open conformation (yellow). B) Free energy landscape represented using the cMDS components. The free energy minima with flipped Leu148 and Phe152 are circled C) Free energy landscape represented using the RMSD of the A-loop from the inactive conformation and the difference in distances between the couples Glu51-Arg150 and Lys33-Glu51. D) Free energy landscape represented using the RMSD of the A-loop and the RMSD of the αC-helix from the inactive conformation. Energies equal or above 30 kcal/mol from the global minimum were cut and represented in white as the background for the sake of clarity.