I would like to compare two homo-dimers. Both Share one identical subunit (which I have aligned structurally) which binds to a second subunit. The specific piece of data I would like to compare is how the second subunits are rotated (measured in degrees) as compared to each other. My question is how does the different but similar dimer interface between the subunits cause the second subunits to rotate/displace in regards to each other.
I am also thinking I can do it by comparing the RMSD values of the second Sub-units but I receive wildly different values depending on the programme used. I think maybe this is a result of the manner of the alignment?
I am most familiar with the programmes Pymol, UCSF Chimera and Swiss PDB.
According to me you may take the center of mass of monomer 1 and monomer 2 in both the cases... get the angle.... it may help......
An RMSD is only going to give you an average distance, I can't see how you might derive an angle from that.
If you superimpose on one subunit and write out the transformed coordinate file (so you have two files which are superimposed on subunit 1), you can then use software such as PDBeFold (www.pdbe.org/fold) or the superposition options in coot to do a superimpose of these files using the second subunit (you will need to specify which residues to superpose in each case, giving each subunit a separate chain ID might be easiest) You will get a rotation/translation matrix output saying exactly how one needs to be moved to overlay on the other.
I've also seen this measurement done by holding a protractor up to the screen!
After superimposition, if the monomer 1 is fixed then the COM1 is fixed and the monomer 2 has 2 COMS (one in the 1st case and other in the 2nd)... Now we have three points and we can calculate the angle.... which can give some sort of idea about the rotation....
Hi Gary,
have you used "measure rot" in UCSF Chimera? It will give you a visual rotation axis and, inside the reply log, the rotation around and the shift along this axis. I think this would be something nice with respect to your problem.
The only thing is that the rotated structures need to be the same in order to use the command directly. If the second monomer of both dimers (the ones that are not aligned; I'll call them 1.2 and 2.2) are the same, then just keep the first monomers (I'll call them 1.1 and 2.1) aligned, split the dimers into four monomers and then use the command to measure the rotation between 1.2 and 2.2. If 1.2 and 2.2 are not the same, you could insert a copy of 1.2 and align it to 2.2 using MatchMaker. Then, using 1.2 and its copy, use measure rotation.
I hope this was kind of clear and that it helps. Otherwise just get back to me.
Cheers,
Michael
Rg (Radius of Gyration) could help to differentiate the TWO states in this case. This is an unusual observation though, where two identical homo-dimers have two binding states. Try calculating, interface area, interface volume and gap index. See if gap index is maintained in both the cases.
Thanks Everyone for your answers so far. I will experiment with your answers this week.
To clarify (Sorry my fault) I wish to compare the heterodimers A:B and A:C. The subunit A is identical in both, the interface is at the same position but slightly different interacting residues and a slight shift in angle between subunits occurs because of the slight change caused by the subunits B and C which are paralogue or homologue proteins.
@Saur- Thanks I am reading the guide and think this may be what I need
@Kumar - What programme do you use to calculate the centre of mass
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