1. Protein Structure and Function 1 , 2 , 3 , 4  Structure Viewing, interpreting structure Protein Characterization BIO520 BioinformaticsJim Lund

2. Protein variety ~100 to >10,000 aa Soluble Integral membrane proteins Membrane-associated Single domain, multiple domains singular, multimeric, large complex

3. Protein Structure 1  structure –aa sequence 2  structure –regular local folding 3  structure –packing and overall folding 4  structure –polypeptide:polypeptide complexes

5. Modifications Proteolysis/processing Residues Modified –cysteine disulfides –phosphorylation –methylation Heteroatoms –Metal ions, heme, cofactors….

6. Dogma Sequence=Structure

7. ,  angles Restricted, but considerable rotation Different residues  different ,  Regular ,  –  helix –  sheet

8. Experimental ,  angles Hovmöller et al., 2002. Conformations of amino acids in proteins

9. An example Ramachandran plot Ideala kinase

10. Forces holding proteins together H-bonding –orientation (dielectric) Hydrophobic effect –nonpolar to core Ionic interaction –+ to -, (dielectric) Dipole effects –  helix, N to C (+ to -)

11.  -helix right-handed aa preferences –A,E,L,M (enriched) –P,G,Y,S (less likely) 3.6 residues/turn helical wheel (amphipathic) dipole N to C

12.  -sheet Parallel or antiparallel N-to-C –Mixed  -sheets are rare: only ~20% of  -sheets are mixed parallel/anti-parallel. “pleated” and “twisted” aa preferences

13.  -turn, loops Length, conformation variable –2 aa hairpins common loops on surface diverge rapidly

14. Simple Super-2 o Motifs hairpin  (  -loop-  ) Helix-loop-helix Greek key (4 antiparallel , wrap)  -  -  motif (  -alpha helix-parallel  )

15. Hairpin 

16. Helix-loop-helix Helix-turn-helix

17. DNA binding EF hand (Ca++ binding)

18. Greek key (4 antiparallel , wrap)

19.  -  -  motif (  -alpha helix-parallel  )

20. Protein Structure Viewers Cn3D (NCBI) –.cn3 files (MMDB, NCBI structures) RasMol –ProteinExplorer –CHIME WWW compatible, animatable –Jmol WWW compatible, animatable

21. Protein Viewing conventions

22. Protein Structure databases MMDB, NCBI structures –Cn3D format (ASN1) Protein Data Bank (PDB) –PDB, Chime, other formats –( http://www.pdb.org)