3D structure of proteins

Question 1

what is the folding of a polypeptide determined by?

Answer 1

→the amino acid sequence
→ the molecular structure and properties of its amino acids
→ the molecular environment (solvent and salts)

Question 2

what is the structure of the peptide bond and what gives the chain movement?

Answer 2

→the peptide bond is a flat planar structure that has a fixed arrangement.
→rotational freedom of the bonds confers movement of the remainder of the chain.

Question 3

what do polypeptides adopt a structure based on? and what does the energy state depend on?

Answer 3

→Polypeptides adopt a structure based on energy minimization.

→Each molecular structure has a specific energy state.

→The minimization 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.

Question 4

what is the free energy of any conformation affected by?

Answer 4

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)

Question 5

what are the forces that determine the folding of a protein? and what are their strengths?

Answer 5

→ COVALENT and NON-COVALENT bonds.

→Weak, non-covalent bonds have 1/20th the strength of covalent bonds.

→overall contribution is significant because the number of non-covalent bonds is far larger than covalent bonds.

Question 6

what are the 4 sub categories of non covalent bonds?

Answer 6

→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.
→ 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

Question 7

what are the properties of disulfide bonds?

Answer 7

→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.

→disulfide bonds can form on the same (intra-chain) or different (inter-chain) polypeptide chains (eg. insulin left).

Question 8

what are the orientation amino acid side-chains in α helices and β sheets?

Answer 8

→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.

Question 9

what is an example of tertiary structure?

Answer 9

→seven transmembrane domain of the thyroid stimulating hormone receptor.

Question 10

what is an example of quaternary structure?

Answer 10

→combining of the four chains of haemoglobin, comprising of 2 α and 2 β chains.

Question 11

what happens to the protein in protein misfolding?

Answer 11

→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.

Question 12

how does protein misfolding happen?

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

how does protein misfolding happen in Alzheimers?

Answer 13

→In Alzheimer’s disease, the proteolytic cleavage of Amyloid Precursor Protein (APP) happens

→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, in the hippocampus.

→higher order insoluble aggregates form which contain much crossed β-structure.

→This becomes deposited in plaques, damaging the neuronal cells of brain.

Question 14

how does protein misfolding happen in cystic fibrosis?2

Answer 14

→the most common mutation is a deletion of Phenylalanine at residue 508 of the cystic fibrosis transmembrane conductance regulator (CFTR) .

→leads to the misfolding of the protein whilst it is still in the ER.

→recognized by the cellular machinery that identifies and processes misfolded protein.

→results in ubiquitination, trafficking of the misfolded protein to the proteasome and degradation.

Question 15

what are infectious proteins and how do they form?

Answer 15

→Prions are misfolded proteins (PrPSC) that interact with other normal proteins (PrPC).

→Through this interaction, they induce misfolding of the normal protein and polymerisation

→Oligomers form fibrils of misfolded 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.