Insights into the Binding Mechanism of Ascorbic Acid and Violaxanthin with Violaxanthin De-Epoxidase (VDE) and Chlorophycean Violaxanthin De-Epoxidase (CVDE) Enzymes: Docking, Molecular Dynamics, and Free Energy Analysis

Photosynthetic organisms have evolved to work under low and high lights in photoprotection, acting as a scavenger of reactive oxygen species. The light dependent xanthophyll cycle involved in this process is performed by a key enzyme (present in the thylakoid lumen) Violaxanthin De-Epoxidase (VDE) in the presence of violaxanthin and ascorbic acid substrates. Phylogenetically, VDE is found to be connected with an ancestral enzyme Chlorophycean Violaxanthin De-Epoxidase (CVDE) present in the green algae on the stromal side of the thylakoid membrane. However, the structure and functions of CVDE were not known. In search of functional similarities involving this cycle, the structure, binding conformation, stability, and interaction mechanism of CVDE are explored with the two substrates in comparison to VDE. The structure of CVDE was determined by homology modeling and validated. In-silico docking (of first-principles-optimized substrates) revealed it has a larger catalytic domain than VDE. A thorough analysis of the binding affinity and stability of four enzyme-substrate complexes are performed by computing free energies and its decomposition, the root-mean-square deviation (RMSD) and fluctuation (RMSF), the radius of gyration, salt-bridge and hydrogen bonding interactions in molecular dynamics. Based on these, violaxanthin interacts with CVDE to the similar extent as that of VDE, hence its role is expected to be the same for both the enzymes. On the contrary, ascorbic acid has a weaker interaction with CVDE than VDE. As these interactions drive epoxidation or de-epoxidation process in the xanthophyll cycle, it immediately discerns that either ascorbic acid does not take part in de-epoxidation or this process requires a different cofactor because of the weaker interaction of ascorbic acid with CVDE in comparison to VDE.