Different approaches to align similar protein structures using the F-ATPases as an example

Aligning F-ATPase alpha and beta subunits

• Start SPdbV
• Open 1bmf.pdb
• Color by Chain
• Change color of chain D to grey/blue (rightclick in control panel on D in first column to select chain D, right click on COL, select color)
• Scroll down the control panel and select all ATP analogs (press ctrl key and right click to select)
• right click on COL in heading and select red color
• Read the pdb file to get info on which chain is which
• select chain F (including nuc) and save selected residues as betaTP.
• select chain A (including nuc) and save selected residues as alphaE.
• After playing with the F1-ATPase, close this file and open betaTP and alphaE.
• Display Layers info [Windows menu]
• select and display only the nucleotides
• There are different ways to align 3-D structures. One way is to select 3 corresponding points in each of the two structures. To do so you can use the substrate molecule.
• Using the mov check off in the Layer Info, reorient the two ANPs so that they are in a similar orientation (but not overlapping).
• Click on the align button on the toolbar (the one with the 3 green and 3 red dots). Notice the red instructions that appear in the header next to the pdb-page icon. Follow these instruction using three corresponding atoms.
• Display all residues in both chains
• Using the mov checks in the Layer info, move the two chains next to each other.
• What do you think about the result?
• Another way to align structures is to use the magic fit in the tools command. Do this and run improve fit (notice the red info in the header)
• Click on alpha in Layer info to make the alpha subunit the active layer
• Color CPK
• Make the beta subunit the active layer
• COLOR rms . The further the atoms in the beta subunit are away from the alpha subunit, the longer wavelengths it is the colored.
• DISPLAY Show alignment window - gives you the aligned sequences.
• How does this alignment compare to the ones calculated using Clustalw?
• If you have time, repeat the exercise for the three beta subunits to observe the structural changes the beta subunit is undergoing in the catalytic cycle.