Characterizing protein protonation microstates using Monte Carlo sampling

ABSTRACT Proteins are polyelectrolytes with acidic or basic amino acids making up ≈25% of the residues. The protonation state of all Asp, Glu, Arg, Lys, His and other protonatable residues, cofactors and ligands define each protonation microstate. As all of these residues will not be fully ionized or neutral, proteins exist in a mixture of microstates. The microstate distribution changes with pH. As the protein environment modifies the proton affinity of each site the distribution may also change in different reaction intermediates or as ligands are bound. Particular protonation microstates may be required for function, while others exist simply because there are many states with similar energy. Here, the protonation microstates generated in Monte Carlo sampling in MCCE are characterized in HEW lysozyme as a function of pH and bacterial photosynthetic reaction centers (RCs) in different reaction intermediates. The lowest energy and highest probability microstates are compared. The ΔG, ΔH and ΔS between the four protonation states of Glu35 and Asp52 in lysozyme are shown to be calculated with reasonable precision. A weighted Pearson correlation analysis identifies coupling between residue protonation states in RCs and how they change when the quinone in the Q B site is reduced.