Protein StructureFall 2011

Aaron Zampaglione

Protein Fold

Rossmann Fold

Protein Domains (Folds)

Four main classes:All-αAll-βα+βα/β(Membrane and cell surface proteins and peptides)(Small proteins)

All-α

The lone helix The helix-turn-helix motif The four-helix bundle Helix-helix packing

All-β

β sandwiches and β barrels Up-and-down antiparallel β sheets β-propellors β-trefoils β-Helix

α+β

Bacterial and mammalian pancreatic ribonucleases

Lysozome Ubiquitin

α/β

α/βhorseshoe α/βbarrels

beta-alpha-beta

Motif

Structural Motifs

β-α-β β-hairpin Greek Key Helix-Loop-Helix (HLH)

Helix-Turn-Helix (HTH) Leucine Zipper Psi-loop Zinc Finger

β-α-β Motif

β-hairpin Motif

Greek Key Motif

Helix-Loop-Helix (HLH) Motif

Helix-Turn-Helix (HTH) Motif

Leucine Zipper Motif

Psi-loop Motif

Zinc Finger Motif

Biology Workbench

Protein Tools Alignment Tools Structure Tools

http://workbench.sdsc.edu

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

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

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