Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: the impact on protein structure, dynamics, and stability

Abstract

Structural and biochemical characterization of protein kinases that confer oncogene addiction and harbor a large number of disease-associated mutations, including RET and MET kinases, have provided insights into molecular mechanisms associated with the protein kinase activation in human cancer. In this article, structural modeling, molecular dynamics, and free energy simulations of a structurally conserved mutational hotspot, shared by M918T in RET and M1250T in MET kinases, are undertaken to quantify the molecular mechanism of activation and the functional role of cancer mutations in altering protein kinase structure, dynamics, and stability. The mechanistic basis of the activating RET and MET cancer mutations may be driven by an appreciable free energy destabilization of the inactive kinase state in the mutational forms. According to our results, the locally enhanced mobility of the cancer mutants and a higher conformational entropy are counterbalanced by a larger enthalpy loss and result in the decreased thermodynamic stability. The computed protein stability differences between the wild-type and cancer kinase mutants are consistent with circular dichroism spectroscopy and differential scanning calorimetry experiments. These results support the molecular mechanism of activation, which causes a detrimental imbalance in the dynamic equilibrium shifted toward the active form of the enzyme. Furthermore, computer simulations of the inhibitor binding with the oncogenic and drug-resistant RET mutations have also provided a plausible molecular rationale for the observed differences in the inhibition profiles, which is consistent with the experimental data. Finally, structural mapping of RET and MET cancer mutations and the computed protein stability changes suggest a similar mechanism of activation, whereby the cancer mutations which display the higher oncogenic activity tend to have the greatest destabilization effect on the inactive kinase structure.

Figure 1

(A) The crystal structure of the wild-type RET kinase in the active form (PDB entry 2IVS). (B) A closeup of structural environment near M918T mutation in the RET kinase. (C) The crystal structure of the wild-type MET kinase in the inactive, autoinhibited form (PDB entry 2G15). (D) A closeup of structural environment near M1250T mutation in the MET kinase.

Figure 2

The RMSD values for C_α atoms from 20-ns simulations with the inactive RET kinase (A) and the active RET kinase. (C) The RMSF values of the RET kinase residues (using original numbering in the PDB entries 1XPD and 2IVS) from 20-ns MD simulations with the inactive RET kinase (B) and the active RET kinase (D). For all panels, time evolution of the WT RET is shown in blue; time evolution of the M918T RET mutant is shown in red.

Figure 3

Analysis of MD simulations with the inactive RET kinase. Time evolution history of the distances between Ca atoms of the residues in the local structural environment of the mutational site. Time evolution of the distances between Ca atoms of the M918T RET and V915 RET (A), M918T RET and S922 RET (B), M918T RET and L923 RET (C), and M918T RET and Y928 RET (D). Time evolution of the distances for the M918 WT RET is shown in blue; time evolution of the distances for the T918 RET mutant is shown in red.

Figure 4

(A) The average structure of the inactive form of the WT RET kinase with M918 residue shown in CPK model. (B) A closeup of structural packing near the mutational site in the inactive WT RET kinase. (C) The average structure of the inactive form of the M918T RET kinase mutant with T918 residue shown in CPK model. (D) A closeup of structural packing near the mutational site in the inactive T918 RET kinase.

Figure 5

(A) The average structure of the ACTIVE form of WT RET kinase with M918 residue shown in CPK model. (B) A closeup of structural packing near the mutational site in the ACTIVE WT RET kinase. (C) The average structure of the ACTIVE form of M918T RET kinase mutant with T918 residue shown in CPK model. (D) A closeup of structural packing near the mutational site in the ACTIVE T918 RET kinase.

Figure 6

(A) The RMSD values for C_α atoms from 20-ns MD simulations with the inactive MET kinase. Time evolution of the WT is shown in blue; time evolution of the M1250T mutant is shown in red. (B) The RMSF values of the RET kinase residues (using original numbering in the PDB entry 2G15) from 20-ns MD simulations with the inactive MET kinase. Time evolution of the WT is shown in blue; time evolution of the M1250T mutant is shown in red.

Figure 7

Analysis of MD simulations with the inactive MET kinase. Time evolution of the distances between Ca atoms of the residues in the local structural environment of the mutational site. Time evolution of the distances between Ca atoms of the M1250T MET and L1245 MET (A), M1250T MET and V1257 MET (B), M1250T MET and S1254 MET (C), and M1250T MET and F1260 MET (D). Time evolution of the distances for the M1250 WT MET is shown in blue; time evolution of the distances for the T1250 MET mutant is shown in red.

Figure 8

(A) The average structure of the inactive form of WT MET kinase with M1250 residue shown in CPK model. (B) A closeup of structural packing near the mutational site in the inactive WT MET kinase. (C) The average structure of the inactive form of M1250T MET kinase mutant with T1250 residue shown in CPK model. (D) A closeup of structural packing near the mutational site in the inactive T1250 MET kinase.

Figure 9

The predicted binding mode of the ZD6474 inhibitor (in blue CPK model) with the WT RET Binding site residues are shown in CPK models. (A) Superposition of the predicted binding mode (in blue stick) with the crystallographic conformation of the ZD6474 inhibitor from the WT complex(default colors, stick model) in the WT RET (B); V804G RET mutant (C); and V804M RET mutant (D).

Figure 10

The correlation between the computed and experimental binding free energies of the ZD6474 inhibitor with WT RET, M918T, V804G, and V804M RET mutants.

Figure 11

Structural mapping of cancer mutations and modeling protein stability effects in the RET kinase. Protein stability differences between the WT RET and RET mutants using CUPSAT (A), FOLDx (B), and MM-GBSA (C). Mapping of cancer mutations into the structure of the RET kinase (D). Negative values of protein stability changes correspond to destabilizing mutations. Mutational sites are in green CPK Ca models. Mutations with the largest destabilization effect are shown in red.

Figure 12

Structural mapping of cancer mutations and modeling protein stability effects in the MET kinase. Protein stability differences between the WT RET and RET mutants using CUPSAT (A), FOLDx (B), and MM-GBSA (C). Mapping of cancer mutations into the structure of the RET kinase (D). Negative values of protein stability changes correspond to destabilizing mutations. Mutational sites are in green CPK Ca models. Mutations with the largest destabilization effect are shown in red.