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Protein FoldsAmit Singh & Doug BrutlagPDB Sizel More than 11,000 released atomic coordinateentriesl About 4.5 new entries per day01000200030004000500060007000800090001970 1980 1990 2000YearNumber of EntriesTasksl Compare all known structures to each otherl Classify and organize all structures in a meaningfulwayl Find common folding patterns and structural motifsl Compute distances between protein structuresl Study interactions between structures and othermolecules (Protein Docking)l Use known structures to predict structure fromsequence (Protein Threading)l Many more ...Overviewl Protein folds• Classification of protein structures• Current databasesl Structure Superposition• Existing methods• LOCK - hierarchical protein structure superposition• 3dSearch - fast secondary structure superpositionl DemonstrationsClassification of Protein Structuresl Class• Similar secondary structure content• All α, all β, α/β, etcl Fold (Architecture)• Major structural similarity• SSE’s in similar arrangementl Superfamily (Topology)• Probable common ancestryl Family• Clear evolutionary relationship• Sequence similarity usually > 25%Classes of Protein Structuresl Mainly αl Mainly βl α/β • Parallel β sheets, β-α-β unitsl α+β• Anti-parallel β sheets, segregated αand β regions• helices mostly on one side of sheetClasses of Protein Structuresl Others• Multi-domain, membrane and cell surface, smallproteins, peptides and fragments, designedproteinsFolds / Architecturesl Mainly α• Bundle• Non-Bundlel Mainly β• Single sheet• Roll• Barrel• Clam• Sandwich• Prism• 4/6/7/8 Propeller• Solenoidl α/β and α+β• Closed» Barrel» Roll, ...• Open» Sandwich» Clam, ...eg. The TIM Barrel FoldA Conceptual Problem ...Fold versus TopologyAnother example:Globin vsColicinDatabases of Foldsl SCOP• Structural Classification of Protein Structures• Manual assembly by inspection• All nodes are annotated (eg. All-alpha, alpha/beta)• Structural similarity search using 3dSearch (Singh and Brutlag)l CATH• Class - Architecture - Topology - Homologous Superfamily• Manual classification at Architecture level• Automated topology classification using the SSAP algorithm(Orengo and Taylor)• No structural similarity searchl FSSP• Fully automated using the DALI algorithm (Holm andSander)• No internal node annotations• Structural similarity search using DALIl PClass• Fully automated using the LOCK and 3dSearch algorithms(Singh and Brutlag)• All internal nodes automatically annotated with commonterms• JAVA based classification browser• Structural similarity search using 3dSearchDatabases of FoldsPCLASS Subsetsαα/β & α+β α+β βSubset ofPClassDemonstrationsl Fold Databases• SCOP (http://scop.stanford.edu/scop)• PClass (http://gene.stanford.edu/PClass)l Structural Alignment Tools• LOCK (http://gene.stanford.edu/lock)• 3dSearch (http://gene.stanford.edu/3dSearch/)• DALI


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Stanford BIOC 201 - Protein Folds

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