摘要
A Monte Carlo simulation method was developed for atomic level calculation of the solvent accessible surface(SAS) area of a protein. As an example, the accessibility value of each atom, as well as all the residues of lysozyme was calculated using this method. The calculated accessibility values were applied to the prediction of intrinsic pK a volumes of Asp52 and Glu35, two embedded residues in the active site of lysozyme. In previous methods, the two active site residues were treated as an entity in calculating the overall free electrostatic energy, with results showing great deviation from the experimental data. With atomic level observation, we revealed that each of these two residues has an exposed ionic atom. A more satisfactory result was obtained by taking this into account. A calculated titration curve closer to the experimental one was obtained by using these more accurately calculated pK a value. Results indicated that individual atoms on embedded residues contributed significantly to overall electrostatic properties.
A Monte Carlo simulation method was developed for atomic level calculation of the solvent accessible surface(SAS) area of a protein. As an example, the accessibility value of each atom, as well as all the residues of lysozyme was calculated using this method. The calculated accessibility values were applied to the prediction of intrinsic pK a volumes of Asp52 and Glu35, two embedded residues in the active site of lysozyme. In previous methods, the two active site residues were treated as an entity in calculating the overall free electrostatic energy, with results showing great deviation from the experimental data. With atomic level observation, we revealed that each of these two residues has an exposed ionic atom. A more satisfactory result was obtained by taking this into account. A calculated titration curve closer to the experimental one was obtained by using these more accurately calculated pK a value. Results indicated that individual atoms on embedded residues contributed significantly to overall electrostatic properties.
