Lecture 27 - The 3D Structure Of Proteins

Question 1

Polar amino acids

Answer 1

Ser: Serine
Thr: Threonine
Cys: Cysteine
Asn: Asparagine
Gln: Glutamine
Tyr: Tyrosine
His: Histidine
Trp: Tryptophan

Question 2

Non-polar/Hydrophobic amino acids (7)

Answer 2

Ala: Alanine
Val: Valine
Phe: Phenylalanine
Pro: Proline
lle: Isoleucine
Leu: Leucine
Met: Methionine

Question 3

Aromantic amino acids (3)

Answer 3

Tyr: Tyrosine
His: Histidine
Trp: Tryptophan

Question 4

Charged amino acids (4)

Answer 4

Acidic alternatively negatively charged
Asp: Aspartic acid
Glu: Glutamic acid

Basic alternatively positively charged
Lys: Lysine
Arg: Arginine

Question 5

Variable side chains indicate properties (5)

Answer 5

• Carboxyl groups COO- –> charged or acidic
• Amine groups NH3+ –> charged or basic
• 2^o Amine NH and Carbonyl C=O groups –> Polar
• Hydroxyl OH- –> Polar
• Hydrocarbon –>Non-polar Hydrophobic

Question 6

Bonds (5)

Answer 6

Each repeating unit of the polypeptide is joined by a peptide bond.
Variable side chain, R is trans conformation.
Planar structure with rotational freedom within molecule found on alpha carbon.
Delocalised electrons of the N-CO make the bond rigid.
Glycines R group (H) allows greater flexibility of the peptide backbone.
Rotational freedom favours structural arrangements, alpha helices and beta sheets.

Question 7

Energy minimisation (7)

Answer 7

• Each molecular structure has a specific energetic state.
• The minimisation of this energetic state (the free energy of a molecule “G”) determines the most favourable arrangement of the atoms (confirmation).
• The change in free energy upon folding is called ∆G.
• The free energy of any conformation is affected by the molecular environment.
o Aqueous or lipid membrane.
o Other proteins or molecules including salts and their ionic state.
o Changes in this environment can induce a further conformational change- for example a receptor binding a ligand.

Question 8

Protein structure (4)

Answer 8

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 and Covalent bonds (as for Tertiary) and sometimes by inter-chain covalent (disulphide) bonds.

Question 9

Bond folding - Non-Covalent bonds (5)

Answer 9

1/20th strength of covalent bonds.
Overall contribution is significant as non-covalent bonds are larger in number.

o Charge or electrostatic attractions
 Falls off exponentially as distance increases, affected by electrostatic environment (aqueous environment).
o Hydrogen bonds
 Occurs between polar groups like the carbonyl (C=O) and amide (NH) groups of the backbone.
o Van der Waals attractions – dipole
 These weak forces occur between two atoms in non-covalent interactions. Determined by their fluctuating charge. Forces are induced by proximity of molecules.
o Hydrophobic interactions
 (Water is a polar molecule) hydrophobic interactions minimise disruption of water network – i.e. the fourth weak force.

Question 10

Bond folding - Covalent bonds (4)

Answer 10

o Disulphide bonds
 Form in oxidative reaction.
 The SH groups from each cysteine cross link.
 Usually occurs in distant parts of the primary sequence but adjacent in the 3D structure.
 Can form on the same (intra-chain) or different (inter-chain) polypeptide chains e.g. insulin.

Question 11

Protein misfolding diseases (8)

Answer 11

• The function of the mis-folded protein is almost always lost or reduced.
• Misfolded proteins tend to self-associate and form aggregates
o Huntingtin Htt (Huntington’s).
o Amyloid-beta Ab (Alzheimer’s).
o Prion protein (PrPSc).
o alpha-synuclein (Parkinson’s disease).
o Serum amyloid A (AA amyloidosis).
o Islet amyloid polypeptide IAPP (Type 2 Diabetes)
• Other mis-folded proteins result in cellular processing that lead to their degradation.
o Cystic fibrosis

Question 12

Misfolding can occur for several reasons (6)

Answer 12

 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.

Question 13

Protein misfolding - Alzheimer’s disease Amyloid hypothesis (9)

Answer 13

• In Alzheimer’s disease proteolytic cleavage of Amyloid Precursor Protein (APP) is observed.
• APP is a large transmembrane protein.
• APP has multiple functions but is involved in G-protein signalling.
• Proteolysis leads to cleavage of APP results in a @40 residue peptide -Amyloid (A).
• Misfolding of this protein results in a planar arrangement and polymerisation.
• This can form fibrils of mis-folded protein (amyloid fibrils).
• β-Amyloid (Aβ) fibres are formed from stacked beta sheets in which the side chains interdigitate.
• The aggregation of b-amyloid in the brains interfere with the workings of the synapse, particularly in the hippocampus.
• Higher order insoluble aggregates form, which contain much crossed -structure which become deposited in plaques, damaging the neuronal cells of brain.

Question 14

Protein misfolding - Cystic fibrosis (5)

Answer 14

Most common mutation is deletion of Phenylalanine at residue 508 of the cystic fibrosis transmembrane conductance regulator (CFTR).
• DF508del leads to mis-folding of the protein whilst it is still in the ER.
• Recognised by the cellular machinery that identifies and processes misfolded protein.
• Results in ubiquitination, trafficking to the proteasome and degradation.
• 70% of Caucasian CF patients harbour this mutation.

Question 15

Induced protein misfolding (7)

Answer 15

• Prions.
• Mis-folded proteins (PrPSC) that interact with other normal proteins (PrPC)
• Through this interaction they induce mis-folding of the normal protein and polymerisation.
• Oligomers form fibrils of mis-folded protein.
• This process is reliant upon the concept of energy minimisation ∆G.
• It is a dynamic process brought about by the interaction of molecules resulting in a more stable aggregated structure.
• PrPc protein and the green alpha helices mis fold to form a beta sheet this in turn induces other PrPc proteins to mis-fold and aggregate.