Hi all,
I'm working with a protein that appears to be a dimer in solution, on SEC in runs as 24 kDa, while the actual mass of a dimer is 30. And I am trying to figure out which dimer is the biological one (it is a regulatory protein but details are uknown). The crystal structure gives me a few options (mol A and B in ASU plus P6122 symmetry), but none of them is really convincing: for deltaGdiss PISA goes from -0.4 to 1.5 kcal/mol. Theoretically, I have two compact dimers (1 and 2) and one elongated (3). In 1, I have two hydrophobic helices interacting and four hydrogen bonds, 1550 A2 buried area (out of 14200 total). This interface applies only to molecule A and its crystallographic mate, equivalent molecules B are too far from each other. Moreover, even in the dimer made of mol A there are channel at the interface. Interface 2 is purely hydrophobic, but at least it's consistent, i.e there are comparable interactions for A-A and B-B pairs, 1850 A2 buried area Interface 3 involves non-crystallographic copies, buried area is 1040 A2. The interacting elements are proline-rich, and there are four main-chain - main chain hydrogen bonds plus two main-chain - side chain ones. Formally, these fragments are not classified as beta-strands, but the association does look like an intermolecular beta-sheet. This dimer is not consistent with the SEC data though. I'm assuming that with an elongated shape it would run as a bigger particle than it actually is, not as a smaller one. So I think I can discard first option but I am still debating on 2 and 3. I'll appreciate your comments on this. Karolina
