Modeling the Insertion of Hexokinase in the Mitochondrial Outer Membrane and its Complex Formation with VDAC

Abstract

Hexokinase (HK), a cytosolic protein, interacts with the mitochondrial outer membrane protein VDAC and plays an important role in cell growth and survival. Overexpression of HK-II in cancer cells increases HK-II-VDAC interactions and prevents apoptosis. Previous biochemical studies have shown that hydrophobic N-terminal residues of HK are important for VDAC binding, while several charged residues of VDAC are crucial for the complex formation. However, it was not clear whether HK directly binds VDAC or this interaction is facilitated by membrane binding of HK. Herein, we present a computational study modeling membrane insertion of HK-II and the HK-II-VDAC complex formation on the membrane surface. To test membrane insertion of HK-II, we used the Highly Mobile Membrane Mimic (HMMM) model of lipids in our MD simulations. Seven out of 10 independent 200 ns simulations showed that the first 10 amino acids of the N-terminus of HK-II insert into the membrane. Subsequent 200 ns conventional MD simulation with a full membrane showed a stable membrane binding of HK-II. The deepest insertion of HK-II is 10 Å below the phosphate plane of the membrane. To further study the interaction between the VDAC and HK-II, we then used atomic resolution Brownian dynamics simulations, where an implicit membrane was created for HK-II based on the model developed in our initial phase of the study. From these simulations we found 2 major distinct binding sites of HK-II in VDAC. The interaction residues of these two binding sites agree with previous mutational experiments. This study provides an atomic-scale model of VDAC-bound HK-II at the surface of the membrane.