Protein titration

The protein titration can be computed in two different level:

1) Ideal level: In this case it is used only the primary sequence of protein and the all equations are solved analytically. The protein ideal titration plot has been computed for the protein chosen by user as the sum of the contribution of its individual ionized sites. In this calculation the spacial configuration of residues are not taken into account. Just the primary sequence is used in this modeling level. In this case the pKa's values were based on reference experimental tables [see Protein Science (2006) 15:1214-1218]. By default it is used the Nozaki and Tanford's table, see Methods in Enzymology (1967) 11:715-734.

2) 3D level: Where the calculations are based on protein structure in the macroscopic model protein, using the Poisson-Boltzmann Equation. The protein 3D titration plot has been computed for the protein chosen by user as the sum of the contribution of its individual ionized sites. In this calculation the spacial configuration of residues are taken into account through of the pka's values of each amino acid. The pKa's values were computed using the MEAD software [see Biochemistry (1990) 29:10219-10225].

In the both levels the outcome is shown as a picture in the PNG format, witch the X axis presents pH values and the Y axis presents the valency at each pH.

After the calculation process, the user can download a text file (ASCII format) which contains a report with the main information about the calculations.

Protein capacitance

The protein capacitance plot has been computed for the protein chosen by user as the sum of the contribution of capacitances of its individual ionized sites. This is an ideal calculation where the spacial configuration of residues are not taken into account. Just the primary sequence is used in this modeling level.

pKa's values were based on reference experimental tables [see Protein Science (2006) 15:1214-1218]. By default it is used the Nozaki and Tanford's table, see Methods in Enzymology (1967) 11:715-734

The outcome is shown as a picture in the PNG format. The associated file name is given by a sequence of random numbers. The X axis presents pH values and the Y axis presents the capacitance at each pH.

After the calculation process, the user can download a text file (ASCII format) which contains a report with the main information about the calculations.