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Enhancing the role of structure in function annotation

Enhancing the role of structure in function annotation Apparently “distant” structure/function relationships between proteins MarkUs – A function annotation server Donald Petrey Markus Fischer Kely Norel. Superfamily. Family. Fold. Hierarchical/discrete categorizations. ●. ●. ●. ●. ●.

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Enhancing the role of structure in function annotation

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  1. Enhancing the role of structure in function annotation Apparently “distant” structure/function relationships between proteins MarkUs – A function annotation server Donald Petrey Markus Fischer Kely Norel

  2. Superfamily Family Fold Hierarchical/discrete categorizations ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

  3. Discrete islands

  4. Continuous space

  5. Fe Mg Mg Zn Zn Spo0F EKILIVDDQ AlaD YIICDVCLC Iron ABC transporter LNIYSARHY Aligned Ska search Spo0F template 1900 proteins 100 folds 280 proteins 40 folds metal sites against PDB Spo0F – flavodoxin like fold AlaD – TIM barrel

  6. NESG TM1055 from T. maritima Putative active site

  7. Coenzyme-A NESG Target TM1055 from T. maritima Formyl-CoA transferase from O. formigenes

  8. SAH from DNA methyltransferase CoA from Formyl-CoA transferase Tyrosine from tyrosyl tRNA synthetase Thiamin diphosphate from DXP synthetase TM1055

  9. NESG Target TM1055 from T. maritima Aromatic moieties

  10. AlaD Functional Residues Limit to specific functions Cavity Lining Residues Spo0F

  11. Spo0F structural neighbors annotated by GO as “metal binding”

  12. Spo0F structural neighbors and residues annotated by UniProt as “metal binding”

  13. Rotavirus capsid protein Sialic acid

  14. Rotavirus capsid protein Sugar clusters

  15. Rotavirus capsid protein structural neighbors annotated by GO as “sugar binding”

  16. Rotavirus capsid protein structural neighbors and residues in contact with bound sugar derivates

  17. Enhancing the role of structure in function annotation Detecting relationships that go beyond classification – amplification Interactive generation and validation of hypotheses Integration of sequence/structure/function information Connecting functional ontologies with individual residues Expert structure-based annotation of protein families Donald Petrey Markus Fischer Kely Norel NESG - Guy Montelione Diana Murray

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  19. Enhancing the role of structure in function annotation Detecting relationships that go beyond classification – amplification Interactive generation and validation of hypotheses Integration of sequence/structure/function information Connecting functional ontologies with individual residues Expert structure-based annotation of protein families Donald Petrey Markus Fischer NESG - Guy Montelione Diana Murray

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