Secondary Proteins Flashcards
What is a polypeptide?
A polymer of amino acid residues linked by peptide bonds (amide linkages)
Describe the peptide bond?
Rigid, planar structure
With 40% double-bind character - due to resonance interactions
What information supports the properties of the peptide bond?
The peptides C-N bond is 0.13 A shorter than its N-C alpha single bond
The C=O bond is 0.02 A longer than normally in aldehydes and ketones
What conformation are most peptide bonds?
Trans (one up and one down in the bond)
The bond is in the amide plane
This is more energetically favourable to avoid steric interferences
Except 10% of Proline - they follow cis peptide bonds
What are torsion angles between peptide groups?
They describe polypeptide chain conformations
The backbone/main chain are the atoms participating in the peptide bonds (no side chains)
Therefore the conformation of the backbone can be described by torsion angles - also calle dihedral angles
What are the torsion angles?
Rotation around C alpha (in the middle) C-N and C-C
ϕ and Ψ angles
They are both defined as 180 degrees when the polypeptide chain is fully extended
The conformational freedom is therefore sterically restrained
What indicates allowed conformations of polypeptides?
Ramachandran Diagram - the sterically allowed ϕ and Ψ angles
What are notable exceptions to the generic areas of the Ramachandran diagram?
Proline is the most conformationally restricted amino acid
Glycine is the least sterically hindered - therefore can assume conformations forbidden to other residues
What are the regular secondary structures of proteins?
Alpha helix
Beta pleated sheet
They are regular as they are composed of sequences of residues with repeating ϕ and Ψ angles
Describe the alpha helix?
Right handed helix Ideal: ϕ=−57° and Ψ=−47° 3.6 residues per turn 5.4 A pitch Avg length 12 residues Avg turns 3.3 = 18 A
Amino acid side chains project outwards to avoid steric clashes
How is the backbone arranged within the alpha helix?
The peptide C=O bond of the nth residue points along the helix axis toward the peptide N—H group of the (n+4)th residue
= strong H bonds almost optimum distance of 2.8 A
What is a property of the alpha helix?
They are amphipathic due to ‘faces’ of side chains
The whole coil is a dipole
How is the alpha helix finished off?
The First 3 N-H and the last 3 C=O are not H bonded
But
They can twist to form an N-cap and a C-cap
= helix capping
Describe the beta-pleated sheet?
They are formed from 2 or more chains/sheets
The Hydrogen bonds occur between neighbouring polypeptide chains to form sheets (two types):
Antiparallel - neighbouring polypeptide chains running in opposite directions (most energetically favourable and stable, reaching full H bond potential)
Parallel - H bonded chains run in the same direction
Describe the measurements of beta pleated sheets?
Each strand of a β sheet has a two-residue repeat with a repeat distance of 7.0 Å
Up to 15 residues, avg of 6 residues
2-22 polypeptide strands, avg of 6 strands
Can be amphipathic
