1.  Protein Structure Fall 2011 Aaron Zampaglione

2. Protein Fold Rossmann Fold

3. Protein Domains (Folds) Four main classes:  All- α  All- β  α + β  α / β  (Membrane and cell surface proteins and peptides)  (Small proteins)

4. All- α  The lone helix  The helix-turn-helix motif  The four-helix bundle  Helix-helix packing

5. All- β  β sandwiches and β barrels  Up-and-down antiparallel β sheets  β -propellors  β -trefoils  β -Helix

6. α+βα+β  Bacterial and mammalian pancreatic ribonucleases  Lysozome  Ubiquitin

7. α/βα/β  α / β horseshoe  α / β barrels beta-alpha-beta

8. Motif

9. Structural Motifs  β - α - β  β -hairpin  Greek Key  Helix-Loop-Helix (HLH)  Helix-Turn-Helix (HTH)  Leucine Zipper  Psi-loop  Zinc Finger

10. β - α - β Motif

11. β -hairpin Motif

12. Greek Key Motif

13. Helix-Loop-Helix (HLH) Motif

14. Helix-Turn-Helix (HTH) Motif

15. Leucine Zipper Motif

16. Psi-loop Motif

17. Zinc Finger Motif

18. Biology Workbench  Protein Tools  Alignment Tools  Structure Tools http://workbench.sdsc.edu

19. Additional Tools  CDART (Motifs)  http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?cmd=rp s http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?cmd=rp s  PROSITE (Motifs)  http://prosite.expasy.org/cgi-bin/prosite/prosite-list.pl http://prosite.expasy.org/cgi-bin/prosite/prosite-list.pl  SCOP (Structure)  http://scop.mrc-lmb.cam.ac.uk/scop http://scop.mrc-lmb.cam.ac.uk/scop  CATH (Structure)  http://www.cathdb.info http://www.cathdb.info

20. References  Expasy. (1999). Tertiary Protein Structure and folds. Retrieved 08 30, 2011, from Expasy: http://swissmodel.expasy.org/course/text/chapter4.htm http://swissmodel.expasy.org/course/text/chapter4.htm  Karadaghi, S. (2011). Protein Domains. Retrieved 08 30, 2011, from Protein Structures: http://www.proteinstructures.com/Structure/Structure/pro tein-domains.html http://www.proteinstructures.com/Structure/Structure/pro tein-domains.html  …