Analysis of water channels by molecular dynamics simulation of heterotetrameric sarcosine oxidase

Abstract

A precise 100-ns molecular dynamics simulation in aquo was performed for the heterotetrameric sarcosine oxidase bound with a substrate analogue, dimethylglycine. The spatial region including the protein was divided into small rectangular cells. The average number of the water molecules locating within each cell was calculated based on the simulation trajectory. The clusters of the cells filled with water molecules were used to determine the water channels. The narrowness of the channels, the average hydropathy indices of the residues of the channels, and the number of migration events of water molecules through the channels were consistent with the selective transport hypothesis whereby tunnel T3 is the pathway for the exit of the iminium intermediate of the enzyme reaction.

Potential of mean force and umbrella sampling simulation for the transport of 5‐oxazolidinone in heterotetrameric sarcosine oxidase

“…The root mean square deviations (RMSD) from the X‐ray structure were 0.15 nm for the Cα atoms of the final structure of the 100 ns equilibration run with the eight flexible C‐terminal residues of the δ‐chain excluded in the RMSD. Thus, the HSO structure was highly stable, as described in a previous study 9 . The final structure of the equilibration run was used for the starting structure of the SMD simulations.…”

“…The calculation conditions in the previous MD simulation 9 were followed in the present study, but the X‐ray structure of the reduced form of HSO bound with no substrates (PDB‐ID 3AD9 7 ) was used for the initial structure. The 963, 404, 200, and 91 amino acid residues of the α‐, β‐, γ‐, and δ‐subunits, respectively, were included.…”

“…Several tunnels have been analyzed for the transport of substrates and products, 7 using the geometry‐based tunnel prediction tool CAVER2 8 . Tunnels T1, T2, and T3 that connect the cavity near FAD and the outer surface of HSO has been proposed to be associated with the migration of the products as follows 7,9 . Sarcosine moves into the large cavity of HSO from the outer surface through tunnels T1, T2, or both, as shown in Figure 2.…”

“…The final products are released from HSO through tunnel T3. Based on the above, and focusing on the product exit channel, a 100‐ns molecular dynamics (MD) simulation has been carried out for the HSO bound with the substrate analogue dimethylglycine 9 . The channel regions for the transport of water were determined from the water density distribution (Figure 1B).…”

A Fragmenting Protocol with Explicit Hydration for Calculation of Binding Enthalpies of Target-Ligand Complexes at a Quantum Mechanical Level

“…To overcome the above limitations of experimental methods, theoretical approaches were developed to help the assignation of water positions. These approaches either assign water positions based solely on solute structures [37] or involve calculation of dynamics [38,39,40,41,42,43,44,45] of water–water interactions. In the present study, a molecular dynamics-based method MobyWat [32,46] will be applied for completion of hydration structures of target-ligand interfaces.…”