Protein Structure and Function

1, 2 , 3 , 4 Structure

Viewing, interpreting structure

Protein Characterization

BIO520 Bioinformatics Jim Lund

Protein variety

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

Protein Structure

• 1 structure– aa sequence

• 2 structure– regular local folding

• 3 structure– packing and overall folding

• 4 structure– polypeptide:polypeptide complexes

Modifications

• Proteolysis/processing

• Residues Modified– cysteine disulfides

– phosphorylation

– methylation

• Heteroatoms– Metal ions, heme, cofactors….

Dogma

Sequence=StructureSequence=Structure

, angles

• Restricted, but considerable rotation

• Different residuesdifferent ,

• Regular , helix sheet

Experimental , angles

Hovmöller et al., 2002. Conformations of amino acids in proteins

An example Ramachandran plot

Ideal a kinase

Forces holding proteins together

• H-bonding– orientation (dielectric)

• Hydrophobic effect– nonpolar to core

• Ionic interaction– + to -, (dielectric)

• Dipole effects helix, N to C (+ to -)

-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

-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

-turn, loops

• Length, conformation variable– 2 aa hairpins common

• loops on surface

• diverge rapidly

Simple Super-2o Motifs

• hairpin (-loop- )

• Helix-loop-helix

• Greek key (4 antiparallel , wrap)-- motif (-alpha helix-parallel )

Hairpin

Helix-loop-helixHelix-turn-helix

Helix-loop-helixHelix-turn-helix

DNA binding EF hand (Ca++ binding)

Greek key(4 antiparallel , wrap)

-- motif(-alpha helix-parallel )

Protein Structure Viewers

• Cn3D (NCBI)– .cn3 files (MMDB, NCBI structures)

• RasMol– ProteinExplorer

– CHIME • WWW compatible, animatable

– Jmol• WWW compatible, animatable

Protein Viewing

conventions

Protein Structure databases

• MMDB, NCBI structures– Cn3D format (ASN1)

• Protein Data Bank (PDB)– PDB, Chime, other formats– (http://www.pdb.org)