protein structure and function

Primary Structure

A sequence of amino acids bonded together by peptide bonds

How do amino acids differ?

By their R group (side chain)

How are peptide bonds formed?

By a condensation reaction

How are peptide bonds broken?

By hydrolysis using water

Relationship between gene complexity and protein diversity

As gene complexity increases, protein functional diversity increases

Why are proteins described as dynamic?

They can move and change conformation to perform functions

Examples of dynamic proteins

Kinesin, actin and myosin

Residue

An amino acid within a peptide chain

Dipeptide

2 amino acids joined together

Tripeptide

3 amino acids joined together

Oligopeptide

Several amino acids joined together

Polypeptide

Many amino acids joined together

Main chain

NH₂-CH-COOH backbone

Side chain

Series of R groups attached to the backbone

What dictates protein structure and function?

The amino acid sequence

Effects of amino acid sequence on proteins

Protein stability, solubility, enzyme activity, recognition and disease

Secondary structure

The local folding of a protein backbone into α-helices and β-sheets

Alpha helix

Common right-handed secondary structure

Beta sheet

Secondary structure composed of β-strands

Cause of alpha helix and beta sheet formation

Different conformations adopted by the protein backbone

Alpha helix

Usually a right-handed helix

Pitch of an alpha helix

The height of one complete turn of the helix

Why do alpha helices form?

To allow optimal hydrogen bonding between main chain groups

Hydrogen bonding in alpha helices

C=O of one residue hydrogen bonds with NH of another residue

Alpha helix hydrogen bond pattern

Residue i bonds to residue i+4

Residues per turn in an alpha helix

3.6 residues per turn

Alpha helix dipole

An overall dipole exists along the length of the helix

Beta sheet

A secondary structure composed of two or more beta strands

Orientation of beta strands

Can be parallel or antiparallel

Typical number of beta strands in a sheet

2 to 22 strands

Typical beta strand length

Up to 15 residues, average about 6

Antiparallel beta sheet

Adjacent strands run in opposite directions

Parallel beta sheet

Adjacent strands run in the same direction

Hydrogen bonding in beta sheets

Provides optimal hydrogen bonding between main chain groups

Why are antiparallel beta sheets more stable?

Hydrogen bonds are straighter and therefore stronger

Mixed beta sheet

Contains both parallel and antiparallel strands

Peptide bond structure

Rigid and planar

Why are peptide bonds rigid?

Partial double bond character caused by electron delocalisation

Percentage of trans peptide bonds

Approximately 99%

Why are cis peptide bonds uncommon?

They create steric clashes between adjacent R groups

Exceptions to trans peptide bond preference

Proline and glycine

Why does peptide bond geometry matter?

It restricts the conformations proteins can adopt

Which backbone bonds can rotate?

The bonds on either side of the alpha carbon

Protein backbone representation

A linked sequence of rigid planar peptide groups

Torsion angle

A dihedral angle describing polypeptide conformation

Phi angle (φ)

Torsion angle around the Cα-N bond

Psi angle (ψ)

Torsion angle around the Cα-C bond

Alpha helix side chain orientation

Side chains point outwards and downwards

Why do alpha helix side chains point outwards?

To avoid steric clashes with the main chain

Amphipathic helix

A helix with both hydrophobic and hydrophilic sides

Why are beta sheets pleated?

To maximise hydrogen bonding potential

Beta sheet side chain arrangement

Successive side chains alternate above and below the sheet

Beta sheet repeat distance

A 2-residue repeat spans approximately 7 Å

Amphipathic beta sheet

A beta sheet containing both hydrophobic and hydrophilic faces

Why are natural beta sheets twisted?

Because of the chirality of L-amino acids

Loop

A connection between secondary structures that lacks regular phi and psi angles

Turn

A more ordered connection between secondary structures

Location of loops and turns

Usually found on the surface of proteins

Flexibility of loops and turns

More conformationally flexible than regular secondary structures

Catalytic protein function

Enzymes catalyse chemical reactions

Structural protein function

Provides support in tissues such as muscle, skin and hair

Signalling protein function

Proteins such as insulin and growth hormone transmit signals

Immune protein function

Antibodies protect against pathogens

Regulatory protein function

Transcription factors regulate gene expression

Transport protein function

Haemoglobin transports oxygen

Poisonous protein function

Toxins produced by organisms such as snakes and spiders

Ramachandran plot

A graph showing allowed phi and psi torsion angle combinations

Why are torsion angles restricted?

Steric hindrance limits possible conformations

Disallowed regions of the Ramachandran plot

Regions where steric clashes occur

Where should most amino acids fall on a Ramachandran plot?

Within allowed regions

Alpha helix Ramachandran angles

Phi = -57° and Psi = -47°

Beta sheet Ramachandran angles

Phi = -120° and Psi = +120°

Why is proline conformationally restricted?

Its side chain covalently links back to the main chain

Typical phi angle of proline

Approximately -60°

Why is glycine more flexible?

It has only a hydrogen atom as its side chain

Effect of glycine on protein conformation

Provides additional degrees of freedom

Steric clash

Unfavourable overlap of atoms occupying the same space

Van der Waals clash

A steric overlap between atoms that prevents certain conformations

Protein folding hierarchy

Folding occurs in a hierarchical fashion

First step of protein folding

Small regions of secondary structure form first

Why do early secondary structures persist

Stabilising forces help retain them

What happens to unstable protein structures?

They unravel and are replaced by more stable conformations

When do tertiary and quaternary structures form?

After stable secondary structures have formed

Protein folding funnel model

Proteins sample many different conformational states during folding

Conformational freedom of unfolded proteins

Very high

Entropy of unfolded proteins

High entropy

Final folded state of a protein

Lowest energy state

Valleys in a folding funnel

Represent populated folding intermediates

Can proteins misfold?

Yes

Entropy

A measure of disorder

What does entropy favour?

Greater disorder

Effect of protein folding on peptide ordering

Folding increases ordering, decreases entropy

How is entropy loss compensated during folding?

Water molecules become more disordered

Cause of protein aggregation during misfolding

Exposed hydrophobic residues stick together, Loss of protein function

List some diseases caused by defective misfolding…

Chaperones

Proteins that assist correct protein folding

How do chaperones help?

Provide chambers and energy to refold misfolded proteins

Antibody structure depends on….

Tertiary and quaternary structure plus disulphide bonds

Antibody chains

Heavy chains and light chains

Antibody domains

Variable domains and constant domains