Abstract: The crystal structure of the SARS 3CL proteinase was used to study the electrostatic and hydrophobic interactions between two monomers. Solving the Poisson-Boltzmann equation the finite difference method was used to calculate the electrostatic potential. The solvent accessible surface model was supplied for the molecular surface and hydrophobicity. The electrostatic and hydrophobic interactions were explored under the condition of different pH values. The results indicated that the electrostatic interaction energy, electrostatic desolvation free energy and hydrophobic desolvation free energy showed smaller values when pH values are between 5.5 and 8.5, which indicated that, under the condition, the electrostatic and hydrophobic interaction were favorable to the stability of SARS 3CL proteinase dimer. For the dimer was the active form of the SARS 3CL proteinase, the pH condition was good for retaining the activity of the enzyme. The proteinase had the highest activity at around pH= 7.0 for the strongest electrostatic and hydrophobic interaction, which was consistent with the experimental results. pH values had more influence on the electrostatic desolvation free energy than on the hydrophobic desolvation free energy, which implied that the electrostatic interaction was the key factor to the instability of SARS 3CL proteinase dimer under acidic or alkali condition.

Key words: SARS 3CL proteinase dimer, Electrostatic interaction, Hydrophobic effect, pH value