secondary structure

what is the secondary structure of a protein?

the local spatial arrangement of polypeptide chain/backbone

what structures can be found in secondary structure?

• alpha helices

• beta sheets

• beta turns

what are hydrogen bonds?

• an type of intermolecular force (IMF)

• type of dipole-dipole attraction when a hydrogen atom bonded to a strongly electronegative atom (e.g. F,O,N) exists in the vicinity of another electronegative atom with a lone pair of electrons (e.g. F,O,N)

• covalent bond between hydrogen atom and electronegative atom makes that compound polar (dipoles)

hydrogen bond diagram

why are hydrogen bonds important in secondary structure?

crucial for forming alpha helices and beta sheets

what is an alpha helix

• coiled, right-handed spiral polypeptide backbone

• every backbone C=O group hydrogen-bonds to the N-H group of the amino acid four residues away

• all backbone amino and carbonyl groups are hydrogen bonded to each other creating stability

which direction do side chains project in an alpha helix

project outwards from helix

how many residues are there per turn in an alpha helix?

3.6 residues (~0.54nm)

what is the rise between each RESIDUE in an alpha helix?

1.5 Å

what is the rise between each TURN in an alpha helix?

5.4Å

what is the ‘pitch’ of an alpha helix?

the distance for one complete turn

how is the pitch calculated?

equal to the product of the rise between two amino acids (i.e. 1.5 Å) and the number of residues per turn (i.e. 3.6)

=5.4

what is the overall dipoles of an alpha helix

N terminus is δ+

C terminus is δ-

which amino acids are alpha helix breakers?

proline and glycine

which amino acids are alpha helix formers (commonly found in alpha helices)?

• methionine

• alanine

• glutamic acid

alpha helix diagram

what is a beta sheet?

• laterally packed beta strands, 5-8 residues long

• hydrogen bonds between carbonyl group (C=O) and amino group (-NH) of adjacent strands

• hydrogen bonds are perpendicular to the backbone chain

• beta strands can either be located in the same polypeptide chain or different

where do hydrogen bonds form in a beta sheet?

hydrogen bonds between C=O and N-H groups on neighbouring strands

In the parallel arrangement, for each amino acid, the N-H group is hydrogen bonded to the C=O group of one amino acid on the adjacent strand, whereas the C=O group is hydrogen bonded to the N-H group on the amino acid two residues along the chain.

what is the distance between adjacent amino acids in a beta sheet strand

3.5 Å

what amino acids are beta sheet formers?

• tyrosine

• isoleucine

• valine

what direction do side chains project in beta sheets

sie chains project above and below the strands

beta sheet diagram

antiparallel vs parallel beta sheets

what is a beta turn?

• a 180° turn involving four amino acid residues

• The C=O group of residue x is hydrogen bonded to the N-H group of residue x + 3

• form sharp u-shaped/hairpin bends located on the surface of proteins, reversing direction of polypeptide backbone

what are the different types of beta turn

β-turns are further divided into classes based on the φ and ψ angles of the residues at positions x + 1 and x + 2

Types I and II are the most common

x+2 residue of type II can only be occupied by glycine

beta turn angles table

why are beta turns useful?

help long polypeptides fold into highly compact structures

connect alpha helices and beta sheets

what amino acids are commonly found in beta turns?

asparagine, glycine and proline

• glycine = lack of side chain, small

• proline = causes rigid, restricted twist through ring structure

how are amino acids labelled in beta turns?

i, i+1, i+2, i+3

where does the hydrogen bond form in beta turn

between carbonyl oxygen (C=O) of residue i and amide hydrogen (-NH) of residue i+3

how many types of beta turn exist?

2 (Type I and II)

in type II the third amino acid must be glycine

difference in dihedral angles (psi and phi) in type I and II beta turns

what is a propensity score?

quantitative tendency/intrinsic preference of an amino acid to adopt a specific conformation

• certain amino acids are observed more frequently than others in different secondary structures

• position of amino acid in relation to neighboruing residues is also important and determines structure

why are some amino acids more common than others in certain secondary structures?

due to R group properties and phi/psi angles that an amino acid can adopt

what amino acids are usually found in alpha helix?

Alanine, Ala

Methionine, Met

Glutamic Acid, Glu

what amino acids are commonly found in beta sheets?

tyrosine, tyr

isoleucine, ile

valine, val

what amino acids are commonly found in beta turns?

asparagine, asn

glycine, gly

proline, pro