I read in this mornings CASP e-mail that T0300 is a dimer. Presumably, two monomeric proteins combining to form a dimer may change conformation. Can the Rosetta approach actually model this?

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I would assume that the hope is that Rosetta can eventually, because from what I understand, Rosetta is for "Protein folding, design and docking", where docking means protein-protein interactions.

It is likely that the conformation of the dimer would be slightly different than that of the monomer, especially if the protein forms a heterodimer, that is, Protein A dimerizes with a different type of protein, B.

To understand the full functionality of the protein, we'd need to know what the dimer (or tetramer, or octomer...) looks like, but even in the monomer form, certain motifs (like well known binding domains or cleavage sites) may become visible, helping to prove the function or mechanism of action of the protein.

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I read in this mornings CASP e-mail that T0300 is a dimer. Presumably, two monomeric proteins combining to form a dimer may change conformation. Can the Rosetta approach actually model this?

Good point! And the answer is yes! As mentioned below, it is really a combination of folding and docking, and Rosetta does both. Phil Bradley has developed new code to explicitly handle symmetric oligomers and he has beautiful looking models for the T0300 dimer which he is submitting today.

Post CASP, we will be using Phil's symmetric folding + docking approach to model the many symmetric oligomers occuring in nature, and the toxic amyloid fibers causing many human diseases. One of the fun things about CASP is that it inspires new methods development--Phil had been thinking about this problem for a while, but it was the T0300 challenge that inspired him to put everything together for this quite general problem.

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