Samaneh Parvaneh - Department of Chemistry, University of Kurdistan, P.O. Box ۶۶۱۷۵-۴۱۶, Sanandaj, Iran
Mehdi Irani - Department of Chemistry, University of Kurdistan, P.O. Box ۶۶۱۷۵-۴۱۶, Sanandaj, Iran

Enzymes are biopolymers and their consisting monomers are amino acids. Amino acidresidues can have different protonation states, depending on the residue neighbors insideenzymes. Assigning right protonation states for amino acid residues is controversial in somecases. The assignment is possible by visual hydrogen bond analysis and using programs likePROPKA[۱]. However, the assigned protonation state might not be exact by these methods.Molecular dynamics (MD) simulation is a powerful method to assign protonation sates ofenzyme residues. This method has been used to assign protonation states of Histidines for threeenzymes [۲] and protonation states of Homocitrate and nearby residues in nitrogenase [۳]. Thephilosophy is that if an incorrect protonation state is employed, the atoms in that residue or innearby residues will move to release steric or electrostatic clashes or to form new favorableinteractions. Therefore, the root mean square deviation (RMSD) will be higher for incorrectprotonation states. In this study, we performed four MD simulations to assign protonation statesof the active site glutamate residues (Glu-۱۵۰ and Glu-۳۰۷) of β-galactosidase (PDB ID۳TTS)[۴]. Glutamates inside enzymes can either be protonated (GLU) or deprotonated (GLH).Our results show that the lowest RMSD values of Glu-۱۵۰ and Glu-۳۰۷ belongs to the GLHprotonation state.

Molecular Dynamics, β-Galactosidase, Protonation State