Diversity of function-related conformational changes in proteins: coordinate uncertainty, fragment rigidity, and...

It was found that the variety of function-related conformational changes ("movements") in proteins is beyond the earlier simple classifications. Here we offer biochemists a more comprehensive, transparent, and easy-to-use approach allowing a detailed and accurate interpretation of such conformational changes. It makes possible a more multifaceted characterization of protein flexibility via identification of rigidly and nonrigidly repositioned fragments, stable and nonstable fragments, and domain and nondomain repositioning. "Coordinate uncertainty thresholds" derived from computed differences between independently determined coordinates of the same molecules are used as the criteria for conformational identity. "Identical" rigid substructures are localized in the distance difference matrices (DDMs). A sequence of simple transformations determines whether a structural change occurs by rigid-body movements of fragments or largely through non-rigid-body deformations. We estimate the stability of protein fragments and compare stable and rigidly moving fragments. The motions computed with the coarse-grained elastic networks are also compared to those of their DDM analogues. We study and suggest a classification for 17 structural pairs, differing in their functional states. For five of the 17 proteins, conformational change cannot be accomplished by rigid-body transformations and requires significant non-rigid-body deformations. Stable fragments rarely coincide with rigidly moving fragments and often disagree with the CATH identifications of domains. Almost all monomeric apo chains, containing stable fragments and/or domains, indicate instability of the entire molecule, suggesting the importance of fragments and domains motions prior to stabilization by substrate binding or crystallization. Notably, kinases exhibit the greatest extent of nonrigidity among the proteins investigated.