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Functional Annotation of uncharacterized proteins in PDB by Swagata N Das

Functional Annotation of uncharacterized proteins in PDB by Swagata N Das. Guided by: 1. Dr. Shuchismita Dutta, Assistant Research Professor, Rutgers University, NJ 2. Dr. Sona Vasudevan , Director , Georgetown University, DC. Process Overview:.

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Functional Annotation of uncharacterized proteins in PDB by Swagata N Das

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  1. Functional Annotation of uncharacterized proteins in PDBby Swagata N Das Guided by: 1. Dr. Shuchismita Dutta, Assistant Research Professor, Rutgers University, NJ 2. Dr. SonaVasudevan, Director, Georgetown University, DC

  2. Process Overview:

  3. Finding the Missing entries (which are already annotated): • To get Accession No RCSB PDB (Web Resource) User Input(human PDB IDs) To get corresponding PDB IDs, Chain and Domain Information To get Classification Details RCSB PDB (Web Resource) UniProt (Web Resource) Analysis Missed Entries (Already Annotated- 62) Unknown Functions -117 Program: Workflow

  4. Missed Case – An Example

  5. Finding Sequence Similarity Seq Similarity: at 50% - PDZ domain

  6. Finding 3D Similarity Pfam:PDZ domain 3D Similarity

  7. SCOP and PFAM Results SCOP: No info, PFAM: PDZ domain

  8. 10 Steps: BLAST

  9. COG Results

  10. CDD domain

  11. Quick Analysis and Inference of Possible Functions RCSB PIRSF COG PFAM CDD BLAST Cn3D PDB ID or FASTA Evidence Possible Functions

  12. PDZ : • 80 -90 AAs • found in Signaling protein • 6 beta strand and 3 alpha helices • FN3 or Fibronectin type III: • 100 AAs • beta sandwich structure • bind to various substances including heparin, collagen , DNA , actin, fibronectinreceptors • cell adhesions, blood coagulation, cell differentiation and migration,maintenance of cellualarcytoskeleton • SH3: • 60 AAs • Beta barrel folded , consists of 6 beta strands • found in proteins of signaling pathway 3 Frequent Domains

  13. Cytokine receptor motif in aligned FN3 structure

  14. Prolin rich ligand binding site in SH3 domain

  15. Protein binding site in PDZ domain

  16. The conserved Serines in all 7 structures Conserved Serines in 7 strs

  17. Gly vs. Ser Thr(1X3D) Ser(1X3D) Ala(1X4X) Gly(1X4X)

  18. Different Surface Residues – Same Protein T in 1X3D A in 1X4X K in 1x5x

  19. Summary 1.Broad Functional annotation of about 110 uncharacterized human proteins2. Even when the overall structure is conserved, if signature seq motifs are missing the functional annotations can not be transferred reliably3.While residues stabilizing the structural fold are highly conserved in a conserved domain cluster, those exposed on the surface may vary – resulting in different functions and/or interactions Other achievements: + Finding the annotated entries in Functional Sleuth+ Finding the Missed Cases

  20. Acknowledgements 1. DrShushismitaDutta- 2.Dr SonaVasudevan3.Dr Mark Danilesen4.Dr Nathan Edwards5. Dr Lai-Su Yeh

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