Comparison of molecular dynamics and superfamily spaces of protein domain deformation.

TitleComparison of molecular dynamics and superfamily spaces of protein domain deformation.
Publication TypeJournal Article
Year of Publication2009
AuthorsVelázquez-Muriel, Javier A., Rueda Manuel, Cuesta Isabel, Pascual-Montano Alberto, Orozco Modesto, and Carazo José-María
JournalBMC Struct Biol
Date Published2009
KeywordsAmino Acid, Amino Acid Sequence, Chemical, Computer Simulation, Models, Molecular, Protein, Protein Structure, Proteins, Sequence Analysis, Sequence Homology, Tertiary

BACKGROUND: It is well known the strong relationship between protein structure and flexibility, on one hand, and biological protein function, on the other hand. Technically, protein flexibility exploration is an essential task in many applications, such as protein structure prediction and modeling. In this contribution we have compared two different approaches to explore the flexibility space of protein domains: i) molecular dynamics (MD-space), and ii) the study of the structural changes within superfamily (SF-space).

RESULTS: Our analysis indicates that the MD-space and the SF-space display a significant overlap, but are still different enough to be considered as complementary. The SF-space space is wider but less complex than the MD-space, irrespective of the number of members in the superfamily. Also, the SF-space does not sample all possibilities offered by the MD-space, but often introduces very large changes along just a few deformation modes, whose number tend to a plateau as the number of related folds in the superfamily increases.

CONCLUSION: Theoretically, we obtained two conclusions. First, that function restricts the access to some flexibility patterns to evolution, as we observe that when a superfamily member changes to become another, the path does not completely overlap with the physical deformability. Second, that conformational changes from variation in a superfamily are larger and much simpler than those allowed by physical deformability. Methodologically, the conclusion is that both spaces studied are complementary, and have different size and complexity. We expect this fact to have application in fields as 3D-EM/X-ray hybrid models or ab initio protein folding.