Tutorial 1 · Tutorial 2

Tutorial 2: Visualizing structural details in the M2 receptor network

In this tutorial, we revisit the M2 receptor from tutorial 1 and show more ways to explore the interaction network. We will split interactions into polar and hydrophobic components, trace residue interactions to the contributing atoms and link the network to a structure viewer for a 3D representation.

Input data

As in the first tutorial, we use the PDB structure 4mqt to generate a network. However, in order to split between polar and hydrophobic contacts, we need to change the import procedure. Click the 'Import network' button in the SenseNet tab. Make sure to select 'PDB structure contacts' in the dropdown menu, then select the path of the 4qmt PDB file. Note that we can give an atom mask and select an interaction type. The default atom mask '.*' selects atoms with any atom name except hydrogens. You can enter any mask that is a valid Java regular expression. We want to use carbon - carbon contacts for the hydrophobic part, so we need to enter 'C.*' as atom mask (without quotes). To load polar contacts as well, we have to add another import panel. Click on the '+' button on the right of the current panel. On the new import panel, load the same PDB file and enter 'O.|N.|CL.*' as the atom mask. This will select any atoms with names starting with 'O', 'N' or 'CL'. Enter 'polar' (or something similar) as interaction type. Finally, click 'OK' to load the network.

Adjusting the network style

If you are using the same session as in tutorial 1, you can select the 'Style' panel to select your previously created style. If the old style is not available, follow the steps from tutorial 1 to color the IXO ligand node red and the 2CU ligand node green. You might notice that some nodes are connected by more edges than one - this is the case when both polar and carbon contacts exist within the structure. Your network should appear as a mix of solid edges (carbon contacts) and dashed lines (polar contacts). If the nodes cluster too close together, try lowering the layout spring coefficient to 1E-5 (Top menu 'Layout - Settings... - Prefuse Force Directed Layout - Default Spring Coefficient).

Visualizing structure

As networks become more complex, it gets harder to build a structural intuition from them. Linking the network to a 3D structure viewer can help keep track of where the nodes and edges are actually located. Please refer to the manual for more information on setting up the viewers. Change to the 'SenseNet' tab and scroll down to the 'Structure visualization' panel. Click 'Connect viewer'. Select one of the viewer options and click 'OK'. The viewer should start shortly - if you get an error, please refer to the manual for troubleshooting hints. On the 'Structure Visualization' panel, click 'Link network'. At the 'Structure File' entry, select the PDB file and click 'OK'. Your PDB structure should now appear in the graphics window of your viewer. Any selection you make in the network will cause the viewer to highlight the residues and interactions you selected. Try selecting a few residues and edges. You can also select multiple objects at once by holding the 'SHIFT' key.

Analysing the binding site network

Until now, we have investigated the network at the residue level. However, in some cases it is useful to have access to the individiual atoms. Thus, SenseNet allows us to freely expand a residue node into its individual atoms and vice versa. As an example, we will analyse the binding mode of the 2CU ligand.

First, go to the Network tab and select the original network that you imported. Make sure to not use any of the subnetworks you created, as we could miss interactions. Then, select the 2CU node. In order to select all neighbors of this node, press 'CTRL+6' (alternatively: Select/Nodes/First Neighbors of Selected Nodes/Undirected). Press CTRL+N to create a new subnetwork from your selection (alternative: Click 'File - New - Network - From selected nodes,all edges'). Once you have a new subnetwork containing only the 2CU node and its neighbors, double click on the 2CU node. The node will be replaced by a set of individual nodes, each representing one ligand atom. Press F5 to adjust the layout. You can see some features of the binding pocket: There is a large central patch of interconnected residues containing TRP-422, ASN-410, TYR-426 and TYR-80. TYR-177 and TRP-422 sandwich the ligand from two sides. Supporting interactions are established by ASN-419, TYR-83, PHE-181 and ALA-414. Four of the eight polar ligand atoms are in range for polar contacts with the protein. You can click on the edges to see the specific interactions displayed in the structure viewer.

Concluding remarks

In this tutorial, we introduced structural analysis techniques based on different interaction types, atom level networks and 3D visualization. You are now ready to start analysing structures on your own and experiment with methods to gather insights from the network.

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