Lecture 5: Elements of protein structure

Question 1

List the levels (4) of protein structure and define what each one means:

Answer 1

Primary – amino acid sequence of a protein

Secondary – local 3D arrangement of a protein chain over a short stretch of adjacent amino acid residues - dominated by α-helix and β-sheet

Tertiary – 3D structure of a complete protein chain

Quaternary – interchain packing for a protein that contains multiple protein chains

Question 2

In what context would we encounter the terms phi and psi?

Answer 2

phi angle = rotation angle around the N–Cα bond

psi angle = rotation angle around the Cα–C’ bond

Context = One way a protein’s 3D structure can be described is by listing the rotation angles found around the bonds of each residue of the protein chain.

Question 3

What is the third main chain bond angle called?

Answer 3

The omega angle.
The angle of rotation around the peptide bond C’ to N
Very limited range, usually close to either 0°or 180°

Question 4

What are some limitations to Phi-Psi rotation?

Answer 4

Phi-Psi angles have limitations in their values because of steric hindrance, e.g.
* Phi rotation can lead to O – O collision
* Psi rotation can lead to NH – NH collisions
Many limits are possible for these rotations.

Question 5

What are the Planar, trans, dipole – peptide bond properties?

Answer 5

For a trans peptide bond, the omega angle is ~180°, Cα on opposite sides

In a cis peptide bond, the omega angle is ~0°, note steric crowding, Cα on same side

Most peptide bonds are trans, ~10% that precede proline may be cis

Question 6

What are the respective bond lengths for amino acids?

Answer 6

The amide bond or peptide bond C-N bond is 0.13Å shorter than Cα-N bond.

C=O is .02 Å longer than those for most ketones and aldehydes

Question 7

What are the key properties of an ɑ-helix?

Answer 7

• 3.6 residues/turn; 5.4Å rise/turn; d = 1.5Å/residue
• spiral is “right-handed”
• side chains point out from the helix axis; help stabilise the a-helix (each separated by 100 degrees)
• stabilising hydrogen bonds, 12-28 kJ/mol (3-7 kcal/mol)
  Phi= ~ - 57°,
  Psi= ~ - 47°
• Some residues are “helix breakers” e.g., glycine, proline
• helix dipole exists, ˜positive at N-terminus

Question 8

What are the key properties of a β-sheet?

Answer 8

• Comprises stretches of residues with a more extended structure than the a-helix. Each section of β structure is called a β-strand
• Hydrogen-bonding occurs between adjacent strands (chains)
• Adjacent chains can form a β-sheet, ≥ two b-strands
• Typically, 2 to 10 strands per sheet
• Average strand length contains ~ 6 amino acid residues
• Each strand may have up to 15 residues
• Two types of chain orientation in adjacent β-strands:
  parallel and antiparallel

Question 9

What is a beta turn and what are the key features?

Answer 9

• Turns are needed to form globular proteins
• often short, hairpin like, involve usually 3 or 4 residues
• Almost 30% protein residues are in turns
• high Gly, Pro content
• hydrogen bond, across the turn is common
• Type I, Type II are very common types
• more than 16 types, given Roman Numeral names

Question 10

What is the N-terminus of the protein?

Answer 10

The amino acid with the unlinked α-amino group (i.e. the first amino acid of the protein chain)

Question 11

What is the C- terminus of the protein?

Answer 11

The amino acid with the unlinked α-carboxyl group (i.e. the last amino acid of the protein chain)

Question 12

Which residues are hydrogen bonds found between in an ɑ-helix?

Answer 12

The carbonyl oxygen of residue “n” and the N–H of residue “n+4”.
O–N distance ~ 2.9Å.