%0 Journal Article
%T Comparison of molecular dynamics and superfamily spaces of protein domain deformation
%A Javier A Vel¨¢zquez-Muriel
%A Manuel Rueda
%A Isabel Cuesta
%A Alberto Pascual-Montano
%A Modesto Orozco
%A Jos¨¦-Mar¨ªa Carazo
%J BMC Structural Biology
%D 2009
%I BioMed Central
%R 10.1186/1472-6807-9-6
%X 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.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.The central dogma of structural biology asserts that the aminoacid sequence has all the information needed for a protein to adopt a structure, and that structure determines function. The connection between sequence and structure has centered a great amount of work and detailed theories of protein folding exist [1], but still predicting structure or function from sequence is a extremely complex task except in cases of high sequence identity between the target protein and a well annotated homolog [2]. There are many cases of non-homologous proteins sharing a given fold or function as well as proteins with reasonably similar sequences having quite different structures.Flexibility seems to play an important role in protein function, as in many cases movements are key for activity. Unfortunately, still less information exists on t
%U http://www.biomedcentral.com/1472-6807/9/6