Many proteins are homo-oligomers in solution. In other words, monomers self-associate to form noncovalently bound dimers, trimers, etc. SDS-PAGE will only show the monomer because the noncovalent interactions are disrupted by the detergent (SDS). The crystal packing may show associations between monomers that are observed in the crystal but not in solution, so you should not rely on the PDB file alone to understand the oligomeric state of the protein. The published literature should have information about this. 

Ligands sometimes bind at the interface between monomers in an oligomeric protein. Sometimes, the catalytic site is at the interface. Ligands do not always bind at the catalytic site. There may be other binding sites, such as for allosteric effectors.

Do not rely only on docking to draw firm conclusions. Docking results should be regarded as hypotheses. Experimental data are needed to test these hypotheses.

Hi Kanti

The coordinate file (if it came from pdb.org) may contain many molecules - depending on how it was (experimentally) determined. If it was determined by crystallography, you will see the structure of the entire asymmetric unit needed to reconstruct (with symmetry operations) the structure of the crystal. Often the asymmetric unit contains more than one macromolecule and intermolecular contacts can look (on first glance) like a oligomer. Do not be afraid to read the paper describing the structure determination.

One of the best ways to determine experimentally if your protein is a monomer or oligomer is to use analytical ultracentrifugation. @Adam is correct when he says that just about everything binds to everything else if you are willing to count interactions with Kd of millimolar or greater. 

If you are only working in silico, your task is difficult. Predictions are only guesses without experimental verification.

hi ,

Regarding the protein, please check the chains of amino acids.

If the protein contain same chains, u can delete one chain and carry out docking studies if active site is at one chain ( u can check that by the presence of bounded ligands in the pdb structure or by binding site analysis)

For docking, please check the active site residues once again. Sometimes there will be mistake in the active site u selected

With regards

Sajin

Hi Kanti,

FIrst at all, do not blindly believe what you see in the screen. As Adam said, there are a lot of proteins that appear as dimer or oligomers in the pdb file but are just crystallographic arrangements that could have no comparison with what happens in solution. For this reason, is meaningless to perform a docking without  a proper knowledge of your system.

One important consideration is that the tendency of many proteins to form dimer or high order oligomers is concentration-dependent!!! For this reason, my first question to you is, in which conditions are you interested? Physiological or in vitro condition?

You can perform dynamic light scattering (DLS) coupled to SEC separation (or in cuvette) to calculate the hydrodynamic radii and see the oligomeric state with high accuracy. On the other hand, you can do 1H DOSY-NMR experiments (you dont need to label the protein). I hope to help you!

thank you all for your answers but I am working on same protein in vitro, and have expressed and purified as a single band on SDS-PAGE( as given in literature). but in PDB files two chains i.e chain A and chain B are given. If I am taking only chain A docking is unsuccessful. Also at pdb.org it is given in asymmetric ( containing two chains) and biological unit( containg chain A). what does that mean and how should I go for docking.

hi,

you are on right track but the reason of your failure might be the closed conformation of the the active site in the crystallized monomer that you took for docking. Please try MD simulation at least for 5 ns which will tell you the dynamics of the molecule near active site. Cluster the trajectory to get an open conformation of enzyme and try redocking. Another possibility could be take any ligand-complex of your initial docking (failed one) and do dynamics in presence of ligand. The protein conformation will relax in the presence of ligand which might orient the active site residues favorable for docking. 

Let me know if you need help in this direction.

Hi Kanti,

To experimentally determine whether the protein is monomeric or dimeric in solution, use Dynamic light scattering (DLS) analysis. This method isn't simple, but very reliable.

Hi Kanti,

Please pay attention to Adam and Kurt's suggestions. Let me word it differently. There are many ways of finding out whether your protein is monomeric/oligomeric in solution. A simple gel filtration with good standards will do it in a straight forward case. There must be a compelling reason to do the docking studies and some insight/hypothesis generated that can be tested experimentally. Since your protein seems to be an enzyme (you mention catalysis), you could ask whether oligomerization is necessary for catalysis? Can you make mutants in the interface (using the pdb coordinates) that affect activity (kcat or Km) or stability (heat or denaturant)? The in silico docking experiments in itself are not really informative. It will merely hint that 20 or so things are possible. Only experiments will reveal the secrets of your protein.

Sorry for the trouble

Hi does anyone know if it is possible to obtain an oligomer from a monomer from the pdb file?