Using various computer software, I have investigated the effects of pH on the total protein charge, permanent and induced dipole moment, and electrostatic potential on the protein surface for five globular proteins (β-lactoglobulin (BLG), bovine (BSA) and human serum albumin (HSA), egg white lysozyme, and equine myoglobin). For the selected properties, I also examined how they were affected by the addition of monovalent electrolyte. I used PROPKA and DelPhiPKa programs to determine the pKa values of amino acid residues (AA) and titration curves of proteins. The titration curves and corresponding isoionic points (pI) for different PDB entries of the same protein agree well within the chosen method, while the results between methods often differ due to different approaches to charge calculation. I have calculated the dipole moments of proteins using PQR files created with the program PDB2PQR. I showed that the functional dependencies for different PDB structures are mostly similar, while the values themselves can be different mainly in acidic and basic pH regions where several AA residues are (de)protonated. I calculated induced dipole moments using fluctuation theory. I investigated how the choice of protein surface (solvent accessible or solvent excluded surface) and the software used for the surface calculation (YASARA or MSMS) affect the magnitude of the induced dipole moment. I have used the program APBS to calculate the electrostatic potential of proteins displayed on the solvent accessible surface. It is shown that the transitions from mainly positive to negative potential agree well with the calculated isoionic points of the proteins. For BLG, it is also shown how the electrostatic potential changes with the concentration of the added monovalent electrolyte.
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