Homology modeling and molecular dynamics simulation of the HIF2α degradation-related HIF2α-VHL complex

Background: Hypoxia-inducible factor 2 alpha (HIF2 alpha), prolyl hydroxylase domain protein 2 (PHD2), and the von Hippel Lindau tumor suppressor protein (pVHL) are three principal proteins in the oxygen sensing pathway. Under normoxic conditions, a conserved proline in HIF2 alpha is hydroxylated by PHD2 in an oxygen-dependent manner, and then pVHL binds and promotes the degradation of HIF2 alpha. However, the crystal structure of the HIF2 alpha-pVHL complex has not yet been established, and this has limited research on the interaction between HIF and pVHL. Here, we constructed a structural model of a 23-residue HIF2 alpha peptide (528-550)-pVHL-ElonginB-ElonginC complex by using homology modeling and molecular dynamics simulations. We also applied these methods to HIF2 alpha mutants (HYP531PRO, F540L, A530 V, A530T, and G537R) to reveal structural defects that explain how these mutations weaken the interaction with pVHL. Methods: Homology modeling and molecular dynamics simulations were used to construct a three-dimensional (3D) structural model of the HIF2 alpha-VHL complex. Subsequently, MolProbity, an active validation tool, was used to analyze the reliability of the model. Molecular mechanics energies combined with the generalized Born and surface area continuum solvation (MM-GBSA) and solvated interaction energy (SIE) methods were used to calculate the binding free energy between HIF2 alpha and pVHL, and the stability of the simulation system was evaluated by using root mean square deviation (RMSD) analysis. We also determined the secondary structure of the system by using the definition of secondary structure of proteins (DSSP) algorithm. Finally, we investigated the structural significance of specific point mutations known to have clinical implications. Results: We established a reliable structural model of the HIF2 alpha-pVHL complex, which is similar to the crystal structure of HIF1 alpha in 1LQB. Furthermore, we compared the structural model of the HIF2a-pVHL complex and the HIF2 alpha. (HYP531P, F540L, A530V, A530T, and G537R)-pVHL mutants on the basis of RMSD, DSSP, binding free energy, and hydrogen bonding. The experimental data indicate that the stability of the structural model of the HIF2 alpha-pVHL complex is higher than that of the mutants, consistently with clinical observations. Conclusions: The structural model of the HIF2 alpha-pVHL complex presented in this study enhances understanding of how HIF2 alpha is captured by pVHL. Moreover, the important contact amino acids that we identified may be useful in the development of drugs to treat HIF2 alpha-related diseases. (C) 2016 Elsevier Inc. All rights reserved.