Quiz 4 Flashcards
Alpha helix characteristics
- 3.6 aa per turn
- Pitch =.54nm per turn
- phi=-57 psi=-47
- H-bonding between C=O of i th residue and H of peptide N-H of i+4 residue
- Strong hydrogen bond
- Common in globular and fibrous proteins
- • In globular proteins α-helices have a span of ~12 residues
3-10 helix
- n = number of residues per helical turn
- N= number of atoms (including H) in the H-bonded loop
- nN
- Pitch = 0.6 nm/turn
- • Thinner and more elongated than α-helix
- Steric interference with R groups
- • Involved in single turn transitions
Why does the polypeptide have a rigid planar structure?
Resonance. There is double bond character between both the N-C bond and the C=O preventing free rotation
What information is determined by the phi and psi angles?
The backbone conformation, as well as steric hindrance between atoms within the polypepdtide
Where is a phi angle?
between N-C bond of polypeptide
Where is Psi angle?
Between C-COOH of polypeptide
Polyproline II helix
- Left handed
- 3 residues per turn
- Pitch = 0.94nm per turn
- No stabilizing H-bonds between main chain groups
- Gly forms polypeptide II helix (either left or right handed since gly is nonchiral)
- Basic structural motif of collagen
The π helix
• 4.4 residues per turn
- • Pitch is 0.52 nm/turn
- • Wider and shorter than α-helix
- • Often result of mutation
- • Typically only one turn in length
The ß sheet
- Composed of one or more β-strands
- Antiparallel β-strand
- Parallel β-strand
- H-bonds form between adjacent strands
- 2 residue repeat distance of 0.7 nm
- Average 6 residues in length
- Globular proteins are known to have from 2 to 22 polypeptide β-strands
Nonrepetitive Structures
- Globular proteins average ~31% α-helix and ~28% β Sheet
- The remaining polypeptide segments have coil or loop conformation
- Some regions are completely disordered
- • Extended charged surface groups
- • Extended peptide chain segments
- • May allow flexible interactions with other molecules
Fibrous Proteins
Highly elongated structures
Secondary structure dominant structural motifs
Functions: Structural, movement
Alpha keratin
found in mammals
beta keratin
Found in birds and reptiles
Alpha keratin structure
- Helix of helices
- Left handed coiled-coil
- Every third or fourth aa has nonpolar or hydrophobic side chain = hydrophobic strip
- Hydrophobic strips in neighboring keratins form dimers
- Rich in cys-disulfide crosslinking of adjacent polypeptide chains
- Protofilaments are formed from two staggered antiparellel rows of coiled-coils
- dimerization= protofibril
Collagen
- Triple helical structure
- Left-handed helices
- Wrapped together in right-handed sense
- Basic unit is called tropocollagen
- Rich in glycine and proline
collagen fibrils
- Tropocollagen pack together into fibrils
- Fibrils are covalently cross-linked through special reactions at lysine residues
What are the nonpolar amino acid residues and where are they found within proteins
Val, Leu, Ile, Met, Phe
What are the charged polar amino acids and where do they occur within proteins?
Arg, His, Lys, Asp, Glu
- Found on the exterior surface of the protein
- When found on the interior, specific functions
- catalysis
- metal ion bonding
what are the uncharged polar aa’s and where are they found within a protein?
- Ser, Thr, Asn, Gln, Tyr, Trp
- Found in both interior and exterior
- When in interior, tend to form hydrogen bonds with each other
Common motifs within proteins
Specific groupings of secondary structures
- BaB (beta alpha beta) motif
- Beta hairpin motif
- Alpha alpha motif
- Greek key motif (beta hairpin folded over to have 4 antiparallel beta sheets
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CATH system
A way to classify domains
CATH
Four Basic Folding patters (Class)
- Mainly alpha helix
- Mainly beta sheet
- Both helices and sheets
- Little helix or little sheet structure
CATH
General domain folding shapes (Architecture)
- Alpha/beta barrel
CATH
Topology is the order in which the secondary structures are connected in the amino acid sequence
CATH
Homology is the goups of proteins with the same topology
Most common alpha domains
multiple helix bundles
Most common folds amongst beta domains
Beta sandwich
Beta barrel
jelly roll or swiss roll
alpha-beta barrels
open beta sheets - most common structure in globular proteins
Rossman fold
A motif found in proteins that bind nucleotides
- Enzyme cofactors FAD, NAD, NADP
- Composed of up to 7 parallel β-strands
- βαβ motif
- A basic residue (Arg or Lys) at the beginning of first β-strand
- An acidic residue (Glu or Asp) at the end of the second β-strand
- Phosphate binding consensus sequence, GXGXXG
- At the topological switch point a crevice is formed
- Forms part of the enzyme’s active site
