Fig. 3.
Energy landscapes of monomeric vs. oligomeric states of proteins. The left-hand side shows a landscape plot and lowest-energy ensemble for each isolated protein. The right-hand side shows the same proteins simulated in the crystal environment, including their oligomeric binding partners. Colors indicate amount of variation in the Rosetta ensemble (blue, low; red, high), highest at loops and ends. In all but the first case, the lowest-energy models deviate significantly from the deposited coordinates locally, near the oligomeric binding sites. a) 1DHN, dihydroneopterin aldolase. Two long loops (see arrows) show similar conformations but much more variability when the rest of the tetrameric ring is not simulated. b) 1GVP, gene V protein from Ff phage. In isolated simulations the hairpin at top right (see arrow) collapses onto the body of the protein, while in the dimer it makes extensive contacts across the interface. Note that another long, protruding hairpin does not collapse. c) 1UTG, uteroglobin. Pairs of interface helices (see arrows) spread apart to form the dimer, rather than the commoner movement of a single chain-terminal helix (as in part d). d) 2HH6, BH3980 from Bacillus halodurans. The C-terminal helix (see arrow) populates two separate and variable positions (the two red ends) in the monomer, one of which matches the experimentally observed position across the dimer interface.