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Classification: understanding the diversity and principles of

Classification: understanding the diversity and principles of. protein structure and function. MCSG 2001 structures. Protein structure classification. Main reference: Robert B. Russell (2002) Classification of Protein Folds. Molecular Biotechnology 20:17-28.

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Classification: understanding the diversity and principles of

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  1. Classification: understanding the diversity and principles of protein structure and function MCSG 2001 structures

  2. Protein structure classification • Main reference: Robert B. Russell (2002) Classification of Protein Folds. Molecular Biotechnology 20:17-28. • Importance: central to studies of protein structure, function, and evolution • Philosophy: phyletic vs. phenetic • Method: structure comparison + human knowledge

  3. Approaches • Hierarchical • Based on the types and arrangements of secondary structures • Unit (level): domain • Domain assignment - structural vs. functional (fold or function in isolation) - automated assignment methods (structure vs. sequence)

  4. Assignment of Class • All a or All b (could be subjective) • a / b (bab unit) or a + b • Other classes

  5. Subjective class assignment

  6. Assignment of Fold • Defined by the number, type, and arrangement of SSEs • Connectivity (e.g. circular permutation, scrambled proteins)

  7. Circular Permutation (CP) B N A C B A C N C D C D ..A..B..C..D.. ..C..D..A..B..

  8. Circular permutation example 1nls (Concanavalin) 1led (Lectin) C N N C

  9. Scrambled protein pairs N C N C 1au1a_ (Interferon-b) 2occc_ (Cytochrome C oxidase)

  10. Assignment of Superfamily • Homologous even in the absence of significant sequence similarity - certain level of structural similarity - unusual structural features - low but significant sequence similarity from structural alignment - key active site residues - sequence similarity bridges • Divergence vs. convergence

  11. Assignment of Family • significant sequence similarity

  12. superfolds, superfamilies, supersites • TIM barrel, Rossmann-like, ferredoxin-like, b-propellers, 4-helix bundle, Ig-like, b-jelly rolls, Oligonucleotide/oligosaccharride binding (OB) fold, SH3-like. • Structure -> function (only 50% correct)

  13. Structure implicates function?

  14. Classification databases • SCOP - careful assignment of evolutionary relationships; homologous vs. analogous • CATH - A:architecture • FSSP - a list of structural neighbors • VAST - NCBI’s Entrez

  15. CATH

  16. Common Folds

  17. Unique Folds

  18. Structure Comparison Growth factor Cytokine • Evolutionary relationship • Structure classification

  19. 9% sequence identity Shapiro & Harris, 2000

  20. Structure Comparison Tools • DALI ( http://www2.ebi.ac.uk/dali/ ) • CE ( http://cl.sdsc.edu/ ) • VAST (http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.html ) • Prosup ( http://www.came.sbg.ac.at ) • FLASH (http://thr.ibms.sinica.edu.tw/flash/)

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