Protein Structure Flashcards
What is secondary structure?
-Local spatial arrangement of a polypeptide’s backbone/main chain atoms with NO regard to side chains
-Regularly repeating folding patterns
-Regular arrangement of main chain and backbone residues
-Arises due to specific angles between key bonds repeating over and over again
What is tertiary structure?
-3-D structure of an entire polypeptide INCLUDING its side chains
-Determined by linear sequence of amino acids
-Unique to a protein (but related proteins can have similar folds)
What is quaternary structure?
spatial arrangement of a protein’s subunits
What is primary structure?
Linear sequence of amino acids
Why does a peptide group have a rigid, planar structure?
What conformation does the peptide group tend to adopt due to its rigidity?
40% double-bond character due to resonance
Trans conformation
What amino acid adopts a cis peptide bond 10% of the time?
Proline due to cyclic side chain
ψ
alpha carbon—carbon bond dihedral/torsion/rotation angle
ϕ
alpha carbon—nitrogen bond dihedral/torsion/rotation angle
What degree is a torsion angle at when the chain is fully extended?
180 degrees
What are the exceptions to the allowed regions on the Ramachandran diagram?
- Gly: only amino acid with no beta carbon atom, less steric hinderance, can adopt forbidden conformations
- Pro: cyclic side chain limits ϕ angles to -60, most restricted amino acid
What are the most common secondary structures? (aka regular secondary structures)
α helix and β sheet
What are the properties of an α helix?
- Right-handed
- Ideal ϕ of -57 and ψ of -47
- 3.6 residues per turn
- Pitch of 5.4 Å
- 1.5 Å between residues
- Hydrogen bonding between carbonyl of n residue and N-H group of n+4 residue
- Side chains project outward and down from helix (avoids steric hinderance and protect backbone)
- Tightly packed core, very stable
What are the properties of a β sheet?
- Two residue repeat with 7.0 Å repeat distance
1a. 3.5 Å between residues - Right-handed twist due to chiral L amino acids
- Hydrogen bond with neighboring chain
What are the 2 types of β sheets?
- Antiparallel β sheet: most common due to linear H bonding with another sheet, neighboring β sheet runs in opposite direction, held together due to high number of H bonds
- Parallel β sheet: chains extend in the same direction, distorted hydrogen bonds, tend to have 5 or more strands
What bonding stabilizes secondary structure?
Hydrogen bonding
What restricts dihedral bonds?
Steric hinderance
What is a random coil (unstructured)?
Chains that do not have regular repeating values
What are the 2 main classifications of proteins?
Fibrous and globular
What is the structure of collagen?
- Polyproline helix (type of secondary structure)
- Extended individual left-handed helices form triple helix
- Amino acid composition: 33% Gly, 15-30% Pro, and 4Hyp (repeating sequence of Gly-Pro-Hyp)
- Cannot create an α helix due to Pro cannot assume the formation and does not have backbone N-H groups for H bonding
- Single helices are bonded in a triple helix with H bonding
What is a reverse turn?
- Not a true secondary structure
- Often found on protein surface
- Single hydrogen bond (n and n+3)
- 3 types
What are the properties of the 3 reverse turn types?
Type I: Carbonyl of amide bond and side chain are trans to each other at alpha carbon 2
Type II: Carbonyl of amide bond and side chain are cis to each other at alpha carbon 2, Gly is often residue 2 to avoid steric hinderance
Type III (310 helix): tighter than Type I and II turns, avoids unfavorable van der Waals interactions by only having 2-3 residues in a turn, residue 1 in turn is usually Pro
What are types of supersecondary structures?
- βαβ motif (very common)
- β hairpin
- αα motif (founded in coiled coil and helix bundles)
—Inclined towards each other b/c side chains interact to maximize van der Waals forces for stability - Greek key motif
—Allows amino acids that are far away in primary structure to be close together in tertiary structure - β barrels
- Helix loop helix (usually α helices, variation of αα motif, do not need to be inclined towards each other, can take different positions in respect to each other)
- Helix turn helix (important in DNA regulation)
- Zinc finger (25-60 amino acids arranged around 1-2 zinc ions)
What stabilizes tertiary structure?
- Hydrophobic effect (buries nonpolar side chains) has the greatest influence on protein stability
- van der Waals interactions between buried side chains
- (Some) H bonding (usually between buried polar residue and backbone)
- A few ion pairs (mostly on surface)
- Disulfide bonds (in secreted or extracellular proteins)
- Metal ion coordination (ex. zinc finger)
What are domains?
- Globular clusters made from 40-200 residues of polypeptide chain
- Folded, structurally independent regions
- Have characteristics of small proteins
- Have discrete functions
- Can evolve independently
- Important for protein classification
