The 3D Structure of Proteins Flashcards
What is the folding of a polypeptide determined by?
- the amino acid sequence
- the molecular structure and properties of its amino acids
- the molecular environment (solvent and salts)
Why is the peptide bond important?
The peptide bond is a flat planar structure that has a fixed arrangement. The rotational freedom of the bonds confers movement of the remainder of the chain.
What do polypeptides adopt a structure based on?
Polypeptides adopt a structure based on energy minimisation.
Each molecular structure has a specific energy state.
The minimisation of this energetic state (the free energy of a molecule “G”) determines the most favourable conformation. The change in free energy upon folding is called ∆G.
What is the free energy of any conformation affected by?
It’s affected by the molecular environment:
- aqueous or lipid membrane
- other proteins or molecules, including salts
- changes in this environment can induce further conformational change (eg. a receptor binding to a ligand)
What two categories do the forces that determine the folding of a protein fall into?
They fall into two categories: COVALENT and NON-COVALENT bonds.
Weak, non-covalent bonds have 1/20th the strength of covalent bonds. However, their overall contribution is significant because the number of non-covalent bonds is far larger than covalent bonds.
List the four categories that non-covalent bonds fall into.
- CHARGED OR ELECTROSTATIC ATTRACTIONS: falls off exponentially as distance increases, is affected by electrostatic environment (aqueous environment)
- HYDROGEN BONDS: transient non-covalent bonds
- VAN DER WAALS ATTRACTIONS - DIPOLE:
These weak forces occur between two atoms in non-covalent interactions. They’re determined by their fluctuating charge, and are induced by the proximity of the molecules.
The attraction at a close distance is balanced by the repulsion due to the proximity that is determined by the Van der Waals radius of an atom. - HYDROPHOBIC INTERACTIONS: hydrophobic interactions minimise disruption of water network
Describe disulphide bonds, an example of covalent bonds.
Disulfide bonds form between the side chains of two cysteine residues.
The bonds form in an oxidative reaction forming very strong covalent bonds. The SH groups from each cysteine cross link.
This usually occurs in distant parts of the amino acid sequence, but occurs adjacently in the three-dimensional structure.
Disulphide bonds can form on the same (intra-chain) or different (inter-chain) polypeptide chains (eg. insulin left).
RECAP: Describe the four categories of protein structure.
1) PRIMARY STRUCTURE: covalent bonds forming polypeptide chain – i.e. order of amino acid residues joined by peptide bonds
2) SECONDARY STRUCTURE: regular folded form, stabilised by hydrogen bonds – e.g. alpha helices, beta sheets and beta turns
3) TERTIARY STRUCTURE: overall 3D structure, stabilised by hydrogen bonds, hydrophobic, ionic and Van der Waal’s forces, and sometimes by intra-chain covalent (disulphide) bonds
4) QUATERNARY STRUCTURE: organisation of polypeptides into assemblies, stabilised by non-covalent bonds (as for Tertiary) and sometimes by inter-chain covalent (disulphide) bonds
Describe the orientation of amino acid side-chains in α helices and β sheets.
Hydrogen bonding occurs between the carbonyl and amide groups of the polypeptide backbone.
The variable side chains protrude outwards from both molecules, the helical α helix and the planar β sheet and participate in folding of the secondary structure.
Give an example of a tertiary structure.
The seven transmembrane domain of the thyroid stimulating hormone receptor.
Give an example of a quaternary structure.
The combining of the four chains of haemoglobin, comprising of 2 α and 2 β chains.
What happens to the protein in protein misfolding?
Firstly, the function of the misfolded protein is almost always lost.
Secondly, misfolded proteins often have a tendency to self-associate and form aggregates (eg. Huntington’s, Alzheimer’s, Parkinson’s disease, etc.)
Other misfolded proteins result in cellular processing that lead to their degradation.
How does protein misfolding occur?
- somatic mutations in the gene sequence leading to the production of a protein unable to adopt the native folding
- errors in transcription or translation leading to the production of modified proteins unable to properly fold
- failure of the folding machinery
- mistakes of the post-translational modifications or in trafficking of proteins
- structural modification produced by environmental changes
- induction protein misfolding by seeding and cross-seeding by other proteins
Describe the protein misfolding in Alzheimer’s disease.
In Alzheimer’s disease, the proteolytic cleavage of Amyloid Precursor Protein (APP) is observed.
β-Amyloid (Aβ) is a small protein released as a result of proteolysis from a larger transmembrane protein known as APP, it then forms multimers with a specific structure. These interfere with the workings of the synapse, particularly in the hippocampus.
Gradually, higher order insoluble aggregates form, which contain much crossed β-structure. This becomes deposited in plaques, damaging the neuronal cells of brain.
Describe the protein misfolding in Cystic Fibrosis.
In Cystic Fibrosis, the most common mutation is a deletion of Phenylalanine at residue 508 of the cystic fibrosis transmembrane conductance regulator (CFTR) .
This DF508del leads to the misfolding of the protein whilst it is still in the ER.
This is recognised by the cellular machinery that identifies and processes misfolded protein.
This results in ubiquitination, trafficking of the misfolded protein to the proteasome and degradation.
