Cerius2·Ludi



7       Working with the Protein Active Site Viewer

 The Cerius2·Active Site Viewer allows you to:

To assist you in performing these activities, the Active Site Viewer provides the following capabilities:

This chapter explains

Topics covered in this chapter include:

Accessing the Protein Active Site Viewer

Viewing and analyzing bound ligands and active sites

Overlaying database search results


Accessing the Protein Active Site Viewer

 Before you begin:

Before you start work with the Active Site Viewer, you should check the following things:

Starting the Active Site Viewer

 To start the Active Site Viewer, complete the following steps:

1.   Select Protein Tools from the Deck Selector popup. The Active Site Viewer menu card appears:

2.   Select Active Site Viewer from the menu card. The Active Site Viewer panel should appear, as illustrated below.

3.   To define the protein model, select the protein as the current model (if it is not already selected), and click the DEFINE Current Model as Protein button. The Active Site Viewer panel displayed below is shown with a protein model defined and one active site selected.


Viewing and analyzing bound ligands and active sites

 The Active Site Viewer allows you to view and analyze both the structure and the environment of bound ligands and active sites. You can do this by:

Obtaining a view of an active site

 To view an active site you use the following tools:

To obtain a view of an active site

The Active Site Viewer panel contains two listboxes side by side. The first listbox under Select Residues From allows you to select one or more subsets of residues depending on what information is available in the PDB file records when the protein was loaded. The second listbox under Selected Residues lists all the residues that are currently selected, with the ones that are actually displayed highlighted.

What is displayed in the Select Residues From listbox depends on the popup selector setting. Three types of residue subsets are available:

Whenever you make a selection in the Select Residues From listbox, the selected item is automatically selected in the protein and highlighted in the color specified by the Color Selected Atoms popup. All the selected residues are also highlighted in the Selected Residues listbox. By clicking in this list box you can change whether or not a particular residue is highlighted. If you only want to see a few residues in a chain, you may find it easier to use the Deselect All button next to this list box to deselect all the selected residues, then click on the few residues you wish to highlight in the display. To center the view on your selection, click the Center View on Selected Atoms button.

You may also select atoms and/or residues by hand in the Model Viewer window using the regular Cerius2 selection tools. You may import the the corresponding residue selection into the Active Site Viewer panel by clicking the Select Residues within ___ Å around Selected Atoms button, with the radius value set to 0.0. This allows you to select one atom in the protein and then see which residue you have selected. You can also expand the selection directly around these atoms by using a radius value greater than 0.0.

When selecting atoms in the Model Viewer window you should be aware that the Active Site Viewer panel does not update automatically with respect to the listbox selections. Any currently selected atoms will be deselected but will retain the display color they were highlighted with. This can be useful for coloring different residues or active sites by different colors. To do this:

1.   Select residues/active sites so they are displayed in the current highlight color.

2.   Deselect the selection by clicking in the Model Viewer window away from any atoms.

3.   Choose a new highlight color from the Color Selected Atoms popup and repeat from step 1.

To avoid leaving your selection colored, click the Deselect All button before clicking in the Model Viewer window. You may also use this afterwards to clean up the Active Site Viewer panel.

Note

Some functionality for displaying the protein is no longer provided in the ACTIVE SITE VIEWER card. These display options and others are now accessed from the PROTEIN DISPLAY card.  

Defining the Active Site for Cerius2 Applications

The previous section discussed using Active Site Viewer to select residues in the protein, including pre-defined active site subsets recorded in the original PDB file. However, the currently defined active site which modules, such as Ludi, refer to is not defined until you click the DEFINE Active Site button. At this point the currently selected protein atoms become the new active site definition. You can select these atoms by hand using the standard selection tools in the Cerius2 model viewer, (for example, by selecting atoms in the view window). However, you will most often define the active site either by first selecting a site from the PDB SITE CARD list or by expanding the selection around a selected ligand inside the active site.

To define an active site by expanding a volume around a ligand you must first select the ligand by either picking a non-protein residue from the NON_PROTEIN RESIDUES list box, or by selecting all atoms in a ligand that is as separate model that has been positioned into the active site. In this latter case the ligand model must be the current Cerius2 model with the protein model also displayed in OVERLAY view mode.

With the ligand model selected, click the Select Residues within ___ Å around Selected Atoms button. This selects all residues within a sphere of the specified radius (in angstroms) around the ligand. These residues will also be automatically listed in the Selected Residues listbox where you can further edit the selection if you wish.

If the ligand selected is still part of the protein (for example, if you selected from the NON-PROTEIN RESIDUES listbox) then you will probably need to extract this ligand from the active site at some time. You can do this by clicking the Extract Ligand button, which is only available when the value of the Select Residues From popup is set to NON-PROTEIN RESIDUES. The ligand is extracted from the protein as a new model and displayed in Overlay mode with the protein. A warning appears in the textport to let you know that the active site definition has been modified to exclude these extracted atoms.

You may wish to extract the ligand as a separate model before defining the active site. When you expand-select around a model (or atoms) that is not part of the protein, only those residues selected that are in the protein become part of the selection. A side effect of the Extract Ligand command is that the new model created is automatically selected as the Template Ligand.

After you have defined the active site for the protein, you can recall the definition by going to the Active Site Viewer control panel, and clicking on the HIGHLIGHT Defined Active Site button. This button is very useful for refining the definiton of the active site.

Analyzing the protein-ligand interaction

Once you have defined the active site, you can analyze the interaction between the protein and the bound ligand. You do so by calculating and displaying hydrogen bonds and close contact information.

Keep in mind that Cerius2 calculates and displays hydrogen bonds and close contacts according to the various preferences specified for these processes. For detailed information about hydrogen bonds and close contacts, see the discussions of build operations and geometry analysis, respectively, in the Cerius2 Modeling Environment book.

To analyze protein- ligand interaction

To analyze the interaction either:

1.   Select Non-Protein Residue from the Active Site From popup (at the top of the Active Site Viewer control panel).

2.   Left-click to select the appropriate residue from the Non-Protein Residues list box.

3.   Click Extract Ligand. This creates a new model containing only the extracted ligand. This ligand is now referred to as the template ligand. Notice that the name of the new model is modelname_residuename and appears as part of the Define Current/Selected Model as Template Ligand control.

Or:

1.   Select or make current the ligand model in the Visualizer panel.

2.   Click the DEFINE CURRENT|SELECTED Model as Template Ligand button with CURRENT or SELECTED as the popup value, depending on how you referenced the ligand model in step 1.

Note

Active Site Viewer no longer has a command to recombine the template ligand with the protein. This function can be performed instead by selecting all the atoms in the ligand, clicking on Edit/Copy followed by Edit/Paste with the protein as the current model.  

With the template ligand defined, you can calculate and display hydrogen bonds and close contacts by checking that the interactions are between the template and protein, then select the Hydrogen Bonds and/or Close Contacts options.


Overlaying database search results

Along with enabling you to view and analyze bound ligands and active sites, the Cerius2 Protein Active Site Viewer also enables you to overlay candidate small molecules on a structure already positioned in the active site by automatically aligning trial ligands to the template ligand. The Protein Active Site Viewer can then assist you in analyzing each candidate and evaluating its potential as an alternative lead compound.

To evaluate a single trial ligand

1.   Define the protein, active site and template ligand as perscribed in the preceding sections.

2.   Select or make current the candidate model in the Visualizer. This model should have hydrogens added.

3.   Ensure that the Automatically Align trial model to template check button is checked.

4.   Define the Trial Ligand by clicking the DEFINE CURRENT|SELECTED Model as Trial Ligand button with CURRENT or SELECTED as the popup value depending on how you referenced the ligand model in step 2.

5.   The Trial Ligand should be aligned in the active site. Set the ...for interactions between selector to TRIAL LIGAND.

6.   Choose to calculate hydrogen bonds and/or close contacts by clicking on the Hydrogen Bonds or Close Contacts check boxes respectively.

To overlay database search results

1.   Load the results from a database search into the Hit List Browser. This can be done by either performing a Catalyst or ISIS database search or opening the Hit List Browser panel and loading models (hits) from an existing SD file. For more details on Database searching refer to Chapter 13, "Performing a Database Query", in the Cerius2·Hypothesis and Receptor Models book.

2.   Check the Display In Model Window option. A new model with the name of the first model in the Hit Browser panel table should appear in the Visualizer.

3.   (Optional) Check the Color Core Atoms option and choose a color other than DEFAULT from the popup selector. This will help you visualize the model when overlayed onto the protein.

4.   Follow the procedure in the section above, To evaluate a single trial ligand, using the model which appeared in the Visualizer panel as a result of step 2.

5.   Use the Hit Browser commands to step through all the database search hits. As you do, the Trial Ligand model is automatically redefined and aligned into the active site with hydrogen bonds and/or close contacts displayed as specified in step 4.



Last updated March 31, 1999 at 04:06PM PST.
Copyright © 1999, Molecular Simulations Inc. All rights reserved.