Determination of the protonation state of the Asp dyad: conventional molecular dynamics versus thermodynamic integration

Abstract

The protonation state of the Asp dyad is important as it can reveal enzymatic mechanisms, and the information this provides can be used in the development of drugs for proteins such as memapsin 2 (BACE-1), HIV-1 protease, and rennin. Conventional molecular dynamics (MD) simulations have been successfully used to determine the preferred protonation state of the Asp dyad. In the present work, we demonstrate that the results obtained from conventional MD simulations can be greatly influenced by the particular force field applied or the values used for control parameters. In principle, free-energy changes between possible protonation states can be used to determine the protonation state. We show that protonation state prediction by the thermodynamic integration (TI) method is insensitive to force field version or to the cutoff for calculating nonbonded interactions (a control parameter). In the present study, the protonation state of the Asp dyad predicted by TI calculations was the same regardless of the force field and cutoff value applied. Contrary to the intuition that conventional MD is more efficient, our results clearly show that the TI method is actually more efficient and more reliable for determining the protonation state of the Asp dyad.

Protein surface roughness accounts for binding free energy of Plasmepsin II‐ligand complexes

“…Titration curves for inhibitors were calculated by the ChemAxon software . Asp 214 of PlmII was set to be protonated at the oxygen atom OD2 as has been previously described . The protonation states of remaining ionizable residues and histidine tautomers in the protein were determined with the program PDB2PQR, which uses PROPKA for the prediction of pKa values .…”

Fast and Reliable Thermodynamic Approach for Determining the Protonation State of the Asp Dyad

“…The TI calculations were performed as we did in our previous study 15 according to the following equation to simulate the process, where the protonated asp dyad was transformed into the unprotonated state:…”

“…On the other hand, the conformational sampling methods, e.g., free energy perturbation (FEP) , and thermodynamic integration (TI) − methods, are very rigorous in calculating the free energy changes solely from proton at different locations, because the fluctuation from conformational flexibility of protein itself is theoretically eliminated in the framework of FEP and TI methods. In particular, we found out in our previous study that the TI method is very reliable in determining the protonation state of the complicate asp dyad system. In comparison to conventional MD method, TI is much more insensitive to versions of force fields and, more importantly, is capable of perceptively capture the small free energy changes simulated by certain force field.…”

“…Even if additional information from the crystal structure, e.g., the interatomic distances between asp dyad's carboxylic oxygen atoms and nearby atoms interacting with them, may be used to rule out unreasonable possibilities, there still remain two possible protonation states that are not easy to determine. 6,15 In principle, the one with lowest free energy among all possible protonation states is most favored. Thus, the determination of protonation state could be achieved according to the free energy changes between possible protonation states.…”

“…Extensive studies ,,,− demonstrated that the two aspartyl residues of the asp dyad function cooperatively with a net charge of −1, i.e., one residue is protonated while the other one is unprotonated, producing four possible protonation states for the asp dyad. Even if additional information from the crystal structure, e.g., the interatomic distances between asp dyad’s carboxylic oxygen atoms and nearby atoms interacting with them, may be used to rule out unreasonable possibilities, there still remain two possible protonation states that are not easy to determine. , …”