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Protein Structure and Function. 1 , 2 , 3 , 4 Structure Viewing, interpreting structure Protein Characterization. BIO520 BioinformaticsJim Lund. ~100 to >10,000 aa Soluble Integral membrane proteins Membrane-associated Single domain, multiple domains - PowerPoint PPT Presentation
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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)
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