Protein Titration Curve Panel

Generate and display a titration curve for one or more proteins.

To open this panel, click the Tasks button and browse to Biologics → Protein Titration Curve.

  • Using
  • Features
  • Additional Resources

Using the Protein Titration Curve Panel

The titration curve for a protein is calculated from the pKa values of titratable groups—individual ionizable residues and termini—by summing the fractional charges of each group at intervals in the pH value. The pKa values for the standard residues are assigned using ProPKA. For all other possible titratable groups, Epik is used, so the pI calculation includes non-standard amino acids. The pI is calculated over the pH range of pH 2 to pH 12. The constitutive charges (salts) are not included in the pI calculations from this panel by default, but you can include them by selecting Include constitutive charges, or generate the titration curve from the command line (see below).

You can calculate the titration curve for multiple proteins in a single run, as each run only takes a few seconds. These curves can then be displayed simultaneously, allowing you to display curves for mutants of a given protein, for example. In addition, the curves of charge vs pH for each titratable group in a protein can be displayed (the "charge profile"). This information shows you which residues are being ionized at a given pH value, for example.

Titration curves can be exported and imported, allowing you to generate as many curves as you wish and display them in any combination. You can also save images of the titration curves and the charge profiles. When generating new curves or importing curves, you also have the choice of adding the new data to the plot or replacing the existing data.

To run a protein titration curve from the command line, you can use the following command. Run the command with -h for more information.

$SCHRODINGER/run -FROM psp pro_titration_curve.py

For information on command options, see pro_titration_curve.py Command Help.

Protein Titration Curve Panel Features

Use protein structure from option menu

Choose the source of the protein structures whose titration curve is to be calculated, from Workspace or Project Table. The number of structures is indicated next to the source. You can generate titration curves for multiple structures in a single run.

Use only selected Workspace residues option

If the structure source is the Workspace and there is a single structure in the Workspace, you can select residues on the structure, and calculate the titration curve for just these residues, by selecting this option.

Include constitutive charges option

Include the constitutive charges (salts) in the pI calculation. By default they are not included.

Generate Titration Curve button

Run the calculation to generate the titration curve. When you click this button, it is replaced with a progress bar and a Cancel button, until the job finishes.

Once a titration curve is generated, this button becomes a menu, from which you can choose to replace the current curves with the new curve (Replace curve), or add the curve to the existing curves (Overlay curve).

Ionizable residues table

This table lists the ionizable residues (and termini), showing the chain, residue name and number along with the pKa of the residue as calculated by ProPKA, and the fractional charge on the residue at the point selected in the titration curve. Selecting a residue in the table zooms in on that residue in the Workspace (provided that the protein is in the project—this will not be the case if you import titration data).

Import Titration Data button

Import titration data from a CSV file. If the display area contains no data, this button opens a file selector, in which you can select one or more data sets to import. If the display area contains data, the button becomes a menu, from which you can choose to replace the existing data (replace curve) or add to the existing data (overlay curve)

Export Titration Data button

Export the titration data to a CSV file. This allows you to store the data and import it, so you can view it later, or overlay several titration curves.

Titration curve option

Show the titration curves in the display area.

Charge profile option

Show the charge profile data for the selected titration curve in the display area. This is a plot of the net fractional charge on each individual residue as a function of pH.

Display area

Display the titration curves for multiple proteins or the charge profile for a single protein, depending on the option selected for display of data.

Selecting a point on a titration curve selects the corresponding protein, displays it in the Workspace, and displays the data for that protein at the selected pH in the ionizable residues table. Pausing the pointer over a point on a curve displays the protein PDB ID, the pH and the total charge at that pH in a tooltip.

Pausing the pointer over a point on a charge profile curve displays the chain name, residue number, and residue name, the pH and the residue fractional charge in a tooltip.

Proteins are not displayed in the Workspace for imported curves, as there is no information on the association of the curve with the protein.

Data labels option

Label the data points on the titration curves with the pH and charge values. This information is also provided in the tooltip for each point.

pI line option

Display the line of zero net charge, which crosses the titration curves at the pI value.

Legend option

For titration curve display, show the plot symbol, the PDB ID, and the isoelectric point (pI) for each curve at the top right of the display area.

For charge profile display, label the curves with the chain name, residue number, and residue name.

pH range boxes and slider

Specify the pH range over which the curve is displayed. You can enter the limits in the boxes, or drag the sliders to change the limits.

Save Image button

Save an image of the display area in EPS, PDF, PS, PNG, or SVG format. Opens a file selector, where you can choose the image format and name the file.

Settings button

Make settings for the titration curve and charge profile plots. Opens the Protein Titration Curve Settings Dialog Box

Reset button

Clear all data from the panel and reset the settings to their default values.

Related Topics