Protein structure Classification.ppt

Protein structure Classification Ole Lund, Associate professor, CBS, DTU. Why classify proteins Number of solved structures grow rapidly Generate overview of structure types Detect similarities (evolutionary relationships) Set up prediction benchmarks Classification schemes SCOP Manual classification (A Murzin) CATH Semi manual classification (C orengo) FSSP Automatic classification (L Holm) Levels in SCOP Class 10 Folds 648 Superfamilies 1007 Families 1699 Murzin et al., 1995 Major classes in scop Classes All alpha proteins Alpha and beta proteins (a/b) Alpha and beta proteins (a+b) Multi-domain proteins Membrane and cell surface proteins Small proteins All alpha: Hemoglobin (1bab) All beta: Immunoglobulin (8fab) Alpha/beta: Triosephosphate isomerase (1hti) Alpha+beta: Lysozyme (1jsf) Folds* Each Class may be divided into one or more folds Proteins which have the same (~50%) secondary structure elements arranged the in the same order in the protein chain and in three dimensions are classified as having the same fold *confusingly also called fold classes Superfamilies Superfamilies are a subdivisions of folds A superfamily contains proteins which are thought to be evolutionarily related due to Sequence Function Special structural features Relationships between members of a superfamily may not be readily recognizable from the sequence alone Families Subdivision of supefamilies Contains members whose relationship is readily recognizable from the sequence (~25% sequence identity) Families are further subdivided in to Proteins Proteins are divided into Species The same protein may be found in several species Families CATH Levels Class Architecture This level is unique to CATH (~30 is defined) Topology ~Fold(/superfamily) in SCOP Homologous Superfamily ~Superfamily(/family) in SCOP http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html Architecture Same overall arrangement of secondary structures Example: The architecture :Two layer be