Lecture 9: A revision of protein structure

Question 1

Reminder about amino acids

Answer 1

Proteogenic amino acid is the name given to the 20 naturally occurring amino acids found in proteins
Proteogenic amino acids are a (alpha) amino acids and have the general formula above
All amino acids (except glycine) are chiral.

Amino acids polymerise to form peptides and proteins

Each amino acid is linked to the next by a peptide (amide) bond during protein translation on the ribosome. In terms of the chemistry, this is a condensation reaction (ie water is released):

Peptides and proteins are synthesised from the N-terminus to the C-terminus
The order of amino acids in the polypeptide chain is known as the protein sequence. This is also called the primary structure of the protein.
The sequence of a protein or peptide is always given from N-terminus (the amino group) to the C-terminus (α-carboxylate group).

The backbone of a protein consists of those atoms which are constant across all amino acids and form a continuous chain

Question 2

The peptide bond is flat (planar)

Answer 2

The equilibrium between the two isomers of the peptide bond results in:

Partial double bond characteristic => planar bond
Reasonably stable bond and modified reactivity of the ketone and amine (nitrogen of peptide bond and carbonyl are less reactive)
Trans isomer most energetically favourable

Question 3

α-helices

Answer 3

• Structure and Properties:
  
  • Alpha-helices involve non-covalent interactions between residues that are close together in the primary sequence.
  • They are right-handed helices with 3.6 amino acids per turn.
  • The pitch of the helix, which is the vertical distance between one turn and the next, is 5.4 Å (0.54 nm).
• Stabilization:
  
  • Helices are stabilized by hydrogen bonds between the backbone amine (NH) of one amino acid and the backbone carbonyl (CO) of the amino acid four residues earlier (i + 4 → i hydrogen bonding).
• Hydrogen Bonding:
  
  • A hydrogen bond is a non-covalent interaction in which the hydrogen covalently attached to one electronegative atom is shared with another electronegative atom that has a lone pair of electrons. In alpha-helices, this involves the interaction between C=O and H-N groups.

Question 4

b-sheets

Answer 4

β-sheets involve non-covalent interactions between residues which may be far apart in primary sequence. Within each strand of a b-sheet, the polypeptide chain is extended

Chains can run parallel to each other (in the same direction) or anti-parallel (in opposite directions). Anti-parallel strands are more common.

b-sheets are stabilised by backbone hydrogen bonds between C=O: on one strand and H-N on the next

In a protein, α-helices and β-sheets are commonly connected together by loops or regions of irregular structure

Question 5

Secondary structure

Answer 5

Elements of secondary structure are regular structures found in proteins and are formed by non-covalent interactions between backbone atoms

Since secondary structure only involves backbone atoms, it is mostly independent of the detailed primary structure of the protein (although some sidechains can promote or inhibit different secondary structures)

The two main types of secondary structure are:
α-helices
β-sheets (and β-turns)

Question 6

Tertiary structure

Answer 6

Tertiary structure encompasses all non-covalent amino acid interactions between amino acids of a single polypeptide chain which are not included in the definition of secondary structure

All interactions between protein sidechains, or between protein sidechains and the backbone are part of tertiary structure

Tertiary structure often involves interactions between residues which are far apart in terms of primary sequence

Question 7

Quaternary structure

Answer 7

Quaternary structure is the name given to the interactions holding multiple polypeptide chains together into one protein.
An example of a protein with quaternary structure is haemoglobin (tetramer).

Each polypeptide chain is called a subunit. Subunits are held together by the same non-covalent interactions as tertiary structure (see next slide) (occasionally covalent bonds can also be important)

Proteins commonly have two subunits (dimers), three subunits (trimers) or four subunits (tetramers), but may have more (eg the eukaryotic proteasome is made of at least 66 subunits)

Question 8

Forces stabilising protein structures

Answer 8

The 3D structure of proteins is stabilized by large numbers of weak non-covalent interactions
Secondary structure is stabilized by hydrogen bonds
Tertiary and quaternary structure are stabilized by:
Hydrophobic interactions (more in SL12101 / SL12011)
Hydrogen bonds
Salt bridges – pairs of acidic and basic amino acids close together in structure (ie interactions between permanent +ve / -ve charges)
van der Waals interactions (dipole-dipole, dipole-induced dipole, London dispersion forces) – interactions between either permanent or transient d+/d- charges
Disulphide bridges (NB these are covalent interactions) – a covalent S-S bond between the sidechain of two cysteines close in space