Conformational Dynamics and Biological Functions: Simulation Studies on Angiotensin-I Converting Enzyme and Voltage-Gated Proton Channel

Abstract

Proteins are flexible and dynamic. One crystal structure alone does not often completely explain biological functions of the protein. The molecular dynamics (MD) simulation is the powerful tool to study the dynamics, activation and inhibition of biomolecules. In order to understand the biological functions of angiotensin-I converting enzyme and the voltage-gated proton channel, the dynamics of these proteins are investigated using MD simulations. We present all-atom molecular dynamics (MD) simulations of sACE with and without ligands. Two types of inhibitors, the competitive and the mixed noncompetitive, were used to model the ligand bound forms. The unrestrained simulations of sACE experienced a large conformational changes of the entrance lips. Particularly, the free sACE underwent multiple conversions between the “closed” and “open” states. Meanwhile, the ligand bound forms were relatively stable at “closed state”. In the mixed noncompetitive inhibition, the heptapeptide bound to the cleft between two subdomains of sACE by hydrogen bonds and kept the cleft being closed forming “dead-end complex”. Thus, the product of enzyme function cannot exit from the active site, and another substrate may not enter the site for next reaction. Our simulation results provide a complete view on opening and closing behaviors of sACE which is considered to be essential to enzyme function. Also, inhibition mechanisms of competitive and mixed non-competitive sACE inhibitors were deeply studied via the MD simulations. The closed state structure of Hv1 was recently solved by the X-ray crystallography. No open structure exists. We used this structure to perform molecular dynamics simulations with electric field and pH conditions to investigate the mechanism of proton transfer in Hv1. We observed a continuous hydrogen-bonded chain of water molecules (a “water wire”) goes through the channel when the channel opens by the moving up of the S4 helix. The increasing of percentage of opening time was consistent with increasing membrane potential. During simulations, the open channel allows unique water molecules pass through the channel but exclude other ions. This indicated Hv1 channel is highly selective for protons. In the line with previous experimental and simulation observations, our results clearly show that forming of the internal water wire for proton transfer and the opening of channel underlie voltage-and pH-gradient sensing.