Lecture 2: Protein structure - Secondary structure

What is the secondary structure of a polypeptide

The hydrogen bonds formed between the backbone atoms, which allow the protein to fold

Includes alpha helices and beta pleated sheets

Structure of an alpha helix

Rod-like with a tightly coiled backbone

Side chains on the outside

Bond length increases by 5.4A per turn

What are the helices stabilised by

Hydrogen bonding between the O (COOH) and H (NH2)

How many residues per turn

3.6 (13 main chain atoms)

Diheadral angles of amino acids in an a-helix

Phi = -57

Psi = -47

Why do a-helices have an electronic dipole

The O in COOH has a higher electronegativity, so pulls electrons away from N-H bonds, making it partially positive

This neutralises the already existent charges of the N and C termini

Structure of beta strands

Fully extended

Distance between adjacent amino acids is 3.5 A

Diheadral angles are

Phi = -120

Psi= +120

How are beta sheets formed

Linking 2 or more beta strands via hydrogen bonding

What are the 2 different arrangements of beta sheets

Parallel and anti parallel

What are the bonds formed in an antiparallel strand

Hydrogen bonds between NH and CO connect the same amino acids on other strands (they’re opposite each other)

Bonds formed in a parallel strand

Each amino acid on one strand hydrogen bonds its 2 amino acids on the adjacent strand

Do Beta sheets have a dipole

No, the dipoles on adjacent amino acids cancel out

Why do beta sheets tend to twist

Because planar beta sheets result in steric clashes between side chains

Twist to minimise conformational energies of the sidechains BUT retain maximum hydrogen bonding

What are the incompatible amino acids for secondary structure

Proline and glycine

Aromatic amino acids are more likely to form

Beta sheets

Aliphatic most likely to form

Alpha helices

What are beta turns

When the amino acid chain loops back on itself so amino acid 1 forms a hydrogen bond with amino acid 4

What is circular dichroism spectroscopy

Technique which uses circularly polarised light to investigate chiral molecules

Why is this useful

Distinguishing protein secondary structure