This tutorial shows how to explore the barnase:barstar interface and its associated electrostatic interactions in more detail. Barnase and barstar form one of the strongest protein-protein complexes with a binding energy of ca. -18 kcal/mole. Electrostatic potentials computed by numerical solution of the finite difference Poisson-Boltzmann equation using the UHBD program will be displayed at the protein-protein interface.

After opening the tutorial page, you should have 2 windows: the Molsurfer window showing a 2-dimensional map of the interface; and the WebMol window showing a 3-dimensional view of the protein-protein complex and the interface.
If you experience problems with Java in Web browser, download the file ms.zip (or copy from /home/client1/data/ms.zip), unzip ms.zip , change directory to ms/ and run the command file start.com )

1. Adjust the colour of the interface in the WebMol window. To do this, choose a color from the menu obtained by clicking on the MeshColor button in the MolSurfer window.
2. In the WebMol window, rotate the proteins to view the interface by holding down the left mouse button and moving the mouse pointer in the WebMol 3D view window. Also try scaling the 3D view by holding down the right button (cmd+mouse_button on Mac) on the 3D view and moving the mouse pointer up (zooming up) or down (zooming down).
3. To view further interface properties, choose the "View" pull-down menu and select "Add/Remove Map". Then select "electrostatic potential A" and "electrostatic potential D" from the "View" menu. These show the distribution of the electrostatic potential on the interface from chain A (barnase, left) and chain D (barstar, right). Rescale the MoSurfer window so that all maps shown are approximately square-shaped.
4. Notice that the electrostatic potential from chain A (barnase) is not positive over the whole interface as might be expected from the representation of the electrostatic potential obtained the SPDBV tutorial. There are small patches of negative electrostatic potential, which correspond to regions of hydrogen bonding across the interface where the hydrogen-bond acceptor groups are in barnase. Analyze the two maps to see the complementarity of electrostatic potentials from chains A and D. Use the 2D and 3D views to identify the amino acid residues in barnase and barstar responsible for the small regions of complementarity with negative potential from barnase at the interface. ( Move the mouse (without clicking) on the 2D maps to see where the points on 2D maps are on the 3D view (a ball colored by the map property) -see also point 2 below for more help).

1. Remove the electrostatic potential maps by deselecting "electrostatic potential A" and "electrostatic potential D" in the "View" pulldown menu. Then select "atomic hydrophobicity A" and "atomic hydrophobicity D" in the "View" menu.
2. The 2D map "atomic hydrophobicity D" shows the atomic hydrophobicity of the chain D (barstar). Atomic hydrophobicity quantifies the energy cost of transferring solvent accessible surface area of the atom from an aqueous environment to octanol; positive values indicate that the atom is hydrophobic, i.e. its solvation by octanol is energetically more favourable than by water, and vice versa. In proteins, carbon atoms are hydrophobic and nitrogen and oxygen atoms are hydrophilic, or polar. Try to locate 2 red regions in the middle of the map "atomic hydrophobicity D" and define which residues they belong to. To do this, click the left mouse button on the 2D map; rescale the 3D view by holding down the right button (cmd+mouse_button on Mac), go back to the 2D window and move the mouse pointer around the red region to figure out around which residue of barstar (chain D) the corresponding ball will be moving around. Then go back to the 3D view and place the mouse pointer on that residue - the label on the right-top of the WebMol window will give you the residue name (D,35(D) and D,39(D) in this case).
3. Similarly, try to locate the names of barnase residues responsible for the red spot near the center of the map "atomic hydrophobicity A" (R,83(A) and R,87(A)).
4. Deselect the current maps in the "View" menu of the MolSurfer window and select the maps "residue hydrophobicity A" and "residue hydrophobicity D" to see that the hydrophobicities of the residues as a whole are also dominantly negative near the center of the interface, i.e. the main interacting residues are not hydrophobic, but hydrophilic.