Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers

Abstract

Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexameric hemocyanin using explicit solvent molecular dynamics simulations. We focus on the variation in solvent cavities and the formation of tunnels in the two conformational states. By employing principal component analysis and CVAE-based deep learning, we are able to differentiate between the dynamics of the deoxy- and oxygenated states of hemocyanin. Finally, our results identify the deoxygenated open conformation, which adopts a stable, closed conformation after the oxygenation process.

Repurposing Amphotericin B: anti-microbial, molecular docking and molecular dynamics simulation studies suggest inhibition potential of Amphotericin B against MRSA

“…Molecular dynamics (MD) simulation is an indispensable tool for the study of macromolecules such as nucleosomes [34], ribosomes [35], membrane proteins, organic solids, proteins-ligand complexes, etc. Thanks to the improvements in force fields that came about through the progress of quantum physics and computational chemistry, the field of protein-ligand docking has undergone significant advancements in the last 40 years [36][37][38][39]. The use of simulation is widespread in investigating the connection between the structure and function of proteins and protein-ligand complexes.…”