Mastering Your Domains
Despite sophisticated algorithms for structural analysis, the final prediction of protein domain content is often remarkably subjective—you know one when you see it. Unfortunately, the reality is more complicated, and different strategies can disagree on how many domains a protein contains and where the boundaries fall, largely due to the absence of a consistent thermodynamic definition of ‘protein domain’.
Porter and Rose attempt to bring clarity to this situation with a formal definition that yields predictions that are generally corroborated by experimental data. Their method entails determining the m-value for a given protein segment, measuring the extent to which that polypeptide is denatured in a given concentration of urea. If the m-value for a protein segment in isolation is roughly equivalent to its m-value within the context of the whole protein—as quantified by a ‘qualifying ratio’ (QR)—that segment can be considered a true, independent domain. 1
The authors developed an algorithm called ‘structure-energy equivalence of domains’ (SEED), which predicts domains by calculating QR values across entire protein sequences. Importantly, SEED's domain boundary determination process emphasizes the energetic contributions of solvent-exposure of backbone surface area, which the authors cite as the dominant energy term in folding, rather than side-chain interactions. SEED accurately mapped nine proteins for which the domain structure had previously been experimentally obtained; importantly, the experimental and SEED results predicted more domains than the leading domain-prediction algorithms, CATH and SCOP. They also saw divergence between results obtained with SEED and CATH for an additional set of 71 proteins, with experimental data generally supporting SEED's predictions when available. These findings generally suggest that many proteins may contain more and smaller individual domains than previously believed.— Michael Eisenstein
Porter, L.L. & Rose, G.D. Proc. Natl. Acad. Sci., USA, Published online 25 May 2012, DOI: 10.1073/pnas.1202604109.