Can Bio3d analyse dimers ?

[Former user]

As I understand bio3D performs NMA on single chains. If a protein is a dimer, how relevant would the results of such an NMA analysis be (comparison of fluctuations of single chains) ? Please let me know if there is a workaround to deal with dimers .....Even if the input structure is a dimer, the residue fluctuations are plotted chain after chain in sequential order in the results...And when I attempted to visualize the trajectory of the NMA on a dimer, I actually could notice the linking of the terminals of the individual chains in the output trajectories .....when the chains in the input were separate entities....Please advice and elaborate on how to deal with dimers on Bio3D NMA.....

Thank you.

[Lars Skjærven]

Currently dimer analysis is not as streamlined as for monomer analysis. But the functionality is there and you can perform NMA / PCA on dimers.

For single PDB NMA:

> pdb = read.pdb("1hiv")
> modes = nma(pdb)
> plot(modes)
> mktrj(modes, mode=7, pdb=pdb)

When you see the C terminal of chain A linked to the N terminal of chain B is just because you don't output the chain ID when writing the PDB file. e.g. in the example above, there is no information about the chain IDs in the modes object. You will therefore need to provide the pdb object to the mktrj() function. This linking you see is only visual (in VMD or pymol), and has nothing to do with the calculation of the normal modes.

For multiple PDB structures:

> pdbs = pdbaln(c("2HS1", "3A2O", "3FX5", "1HIV"))
> pdbs$xyz = pdbfit(pdbs, outpath="pdbfit")
> pc.xray = pca(pdbs)
> modes = nma(pdbs)
> plot(modes)

For some multimers you will see that the chains are not in the same order in the PDB file relative to each other, so you will have to rearrange them manually using trim.pdb and cat.pdb.

Let me know how it works out, and please provide running examples to illustrate your issue next time.