reconstruction of protein backbones from the brix collection of canonical protein fragments重建的蛋白骨干白利规范化蛋白质片段的集合.pdfVIP

Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments 1,2 1,2 3 3 1,2 3 Lies Baeten , Joke Reumers , Vicente Tur , Franc¸ois Stricher , Tom Lenaerts , Luis Serrano , Frederic Rousseau1,2*, Joost Schymkowitz1,2* 1 SWITCH Laboratory, Vrije Universiteit Brussels, Brussels, Belgium, 2 VIB, Vrije Universiteit Brussels, Belgium, 3 Center for Genomic Regulation, Barcelona, Spain Abstract As modeling of changes in backbone conformation still lacks a computationally efficient solution, we developed a discretisation of the conformational states accessible to the protein backbone similar to the successful rotamer approach in side chains. The BriX fragment database, consisting of fragments from 4 to 14 residues long, was realized through identification of recurrent backbone fragments from a non-redundant set of high-resolution protein structures. BriX contains an alphabet of more than 1,000 frequently observed conformations per peptide length for 6 different variation levels. Analysis of the performance of BriX revealed an average structural coverage of protein structures of more than 99% within a root mean square distance (RMSD) of 1 Angstrom. Globally, we are able to reconstruct protein structures with an average accuracy of 0.48 Angstrom RMSD. As expected, regular structures are well covered, but, interestingly, many loop regions that appear irregular at first glance are also found to form a recurrent structural motif, albeit with lower frequency of occurrence than regular secondary structures. Larger loop regions could be completely reconstructed