Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

20
Protein Structure Fall 2011 Aaron Zampaglione

Transcript of Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Page 1: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Protein StructureFall 2011

Aaron Zampaglione

Page 2: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Protein Fold

Rossmann Fold

Page 3: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Protein Domains (Folds)

Four main classes:

All-α

All-β

α+β

α/β

(Membrane and cell surface proteins and peptides)

(Small proteins)

Page 4: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

All-α

The lone helix

The helix-turn-helix motif

The four-helix bundle

Helix-helix packing

Page 5: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

All-β

β sandwiches and β barrels

Up-and-down antiparallel β sheets

β-propellors

β-trefoils

β-Helix

Page 6: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

α+β

Bacterial and mammalian pancreatic ribonucleases

Lysozome

Ubiquitin

Page 7: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

α/β

α/βhorseshoe

α/βbarrels

beta-alpha-beta

Page 8: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Motif

Page 9: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Structural Motifs

β-α-β

β-hairpin

Greek Key

Helix-Loop-Helix (HLH)

Helix-Turn-Helix (HTH)

Leucine Zipper

Psi-loop

Zinc Finger

Page 10: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

β-α-β Motif

Page 11: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

β-hairpin Motif

Page 12: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Greek Key Motif

Page 13: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Helix-Loop-Helix (HLH) Motif

Page 14: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Helix-Turn-Helix (HTH) Motif

Page 15: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Leucine Zipper Motif

Page 16: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Psi-loop Motif

Page 17: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Zinc Finger Motif

Page 18: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Biology Workbench

Protein Tools

Alignment Tools

Structure Tools

http://workbench.sdsc.edu

Page 19: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

Additional Tools

CDART (Motifs) http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi

?cmd=rps

PROSITE (Motifs) http://prosite.expasy.org/cgi-bin/prosite/prosite-list.pl

SCOP (Structure) http://scop.mrc-lmb.cam.ac.uk/scop

CATH (Structure) http://www.cathdb.info

Page 20: Protein Structure Fall 2011 Aaron Zampaglione. Protein Fold Rossmann Fold.

References

Expasy. (1999). Tertiary Protein Structure and folds. Retrieved 08 30, 2011, from Expasy: 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/protein-domains.html