What do loops and turns do?
Connect alpha helices and Beta strands and allow a peptide chain to fold back on itself to make a compact structure
What are loops?
Connections which often contain hydrophilic residues and are found on protein surfaces
What are turns?
Loops containing 5 residues or less
What are tertiary structures primarily stabilised by?
Non-covalent interactions between side chains
What, apart from non covalent interactions between side chains, stabilises tertiary structures?
How many amino acids in each alpha helix turn?
What are supersecondary structures/ motifs?
Recurring folding patterns comprising at least 2 connected secondary structure elements
What are the 8 motifs?
Helix-loop-helix (2 helices connected by turn)
Coiled-coil (2 helices that interact in parallel through their hydrophobic edges)
Helix bindle (several alpha helices that associate antiparallel manner to form bundles)
B-alpha-B unit (2 parallel B strands linked to alpha helix by 2 loops)
Hairpin (2 anitparralel B strands connected be a B turn)
B meander (antiparallel sheet made of B strands connected by loops or turns)
Greek key (4 antiparallel strands - 1,2 in middle, 3,4 on outside)
B sandwich (stacked B strands or sheets)
What are domains?
- Independently folded compact units in proteins
- 25 to 300 amino acid residues
- Domains can be connected by loops and associated together by non-covalent interactions between side chains
What do domains do?
Domains usually have a stand alone function. Can combine domains for multi-function protein.
What can domains show us?
Can show evolutionary conservation of protein structure. A domain fold can be conserved in many proteins shen the primary structur is undetectable different.
What are the 4 common domain folds?
- Parallel twisted sheet
- alpha/beta barrel
- B helix
What do folding patterns allow us to do?
Classify protein structure into 4 categoriees with common domains and motifs
What are the 4 categories of protein structure?
- All alpha
- All beta
- Mixed alpha/beta (alternating alpha and beta bits)
- Alpha and beta (cluster of alpha then beta seperate)
What are quaternary structures?
Organization of subunits. Subunits have defined stoichiometry and arrangement.