W9.2_Tertiary Structure of Proteins

Question 1

How do secondary structures connect to form tertiary structures? Contrast the structures of loops and turns. Define motif, domain, and subunit.

Answer 1

• Secondary structures connect (through loops/bends) and fold (through non-covalent/covalent forces) to form tertiary structure
• Loops: stretch of exposed hydrophilic residues on surface of proteins to increase flexibility/solubility in water, connect to α-helices and ß-sheets with no regular/repetitive structure
• Turns: loops but <5 residues, most common as ß-turns
• Motif: typical arrangement of ≥2 2o structures (ex. ß-α-ß, ß-ß, α-loop-α, rarely charged in loops to bind with ions)
• Domain: contains many motifs and folded to give a stable, self-contained tertiary structure
• Subunit: combine many domains

Question 2

Explain the different bonding forces that hold proteins together.

Answer 2

• Covalent (disulphide bond): strongest side chain interaction (Cys) through oxidation
• Hydrogen bonds: most important inside protein, protected from exchange with water molecules
• Hydrophobic bonding: ∆G=∆H-T∆S (stable system if ∆G = -ve -> ∆G is desirable when ∆S is high)
• Non-polar compound in water -> loose H-bond network of water lose entropy to rearrange around H2O molecules to maintain total H-bonding energy -> hydrophobic side chain cluster together to avoid H2O -> minimum surface area presented to H2O -> some H2O molecules liberated from solvation shell -> increase entropy
• Van der Waals’ forces: uneven distribution of e- atoms -> attract one another until they reach Van der - Waals’ distance (closer -> repel), very weak, but lots of them can mount up
• Ionic & electrostatic forces: E=(Z+ x Z-)/(p x r) (Z+/Z-: charges, p: dielectric constant (low at non-polar solvent, high at polar solvent, r: distance2
• Two oppositely charged molecules (including δ+/δ-) attract
• Higher E (energy of interaction) value: favourable, stronger forces

Question 3

Describe how secondary structures of proteins collapse into conformations to form tertiary structures. In what cases where the structure would be reversed?

Answer 3

• Hydrophobic interaction favours contact between non-polar aliphatic R groups (in hydrophobic core)
• Hydrophilic R groups on outside of membrane -> exposed to solvent to allow interactions by forming different bonds with other molecules (may change protein structure)
• Packing of aliphatic/hydrophobic groups in internal core and polar groups exposed to water to form hydration shell surrounding protein (main driving force: increase in entropy when hydrophobic groups are buried inside)
• Reverse (hydrophobic out and hydrophilic in) for membrane proteins and ion channels due to environment/function

Question 4

Describe the positions and functions of different amino acids in globular and membrane proteins.

Answer 4

• Non-polar amino acids:
• Globular proteins: interior to form hydrophobic core
• Membrane proteins: surface to anchor with lipid chains
• Polar, charged amino acids:
• Globular proteins: usually surface/interior for catalytic sites
• Membrane proteins: extra membranous/electrostatic interaction/functional groups/form hydrophilic core
• Polar, neutral amino acids:
• Globular proteins: surface/interior for H-bond network
• Membrane proteins: surface/inside of channel, H-bond network

Question 5

Contrast the structure and function of fibrous and globular proteins with the use of examples.

Answer 5

• Fibrous proteins: long fibres/sheets, strong, insoluble in water, structural role, largely one type of 20 structure
• Globular proteins: spherical, delicate, soluble in water, diverse roles (catalysis/storage/immune defence), usually contains both α-helices and ß-sheets
• Ex. myoglobin (non-allosteric, tertiary), haemoglobin (allosteric, quaternary)

Question 6

Describe the structure and function of myoglobin. How is the Fe ion in the centre bonded to different groups and why?

Answer 6

• Myoglobin: O2 storage proteins in skeletal muscle
• Contains a haem prosthetic group/cofactor where O2 binds
• Has hydrophobic residues inside, hydrophilic residues outsides, prolines mainly in bends
• Fe ion: 6 coordination bonds (4 taken by N atoms, 1 by histidine, leaving one for functional reasons)
• Proximal His bonded to Fe, while distal His not bonded to Fe
• Provides O2 binding site with other functional reasons

Question 7

Explain how oxygen is bound to the coordinate site in myoglobin and its related elctron transfer process. What is the role of the protein?

Answer 7

• Coordinate site to bind O2: electron density changes around Fe (partial e- transfer to O), making Fe smaller to fit in
• Partial electron transfer from Fe2+ to O2 might give Fe3+ if complete -> O2 released as superoxide
• ∴ Protein prevents this by Fe2+-O=O <-> Fe3+-O-O-
• Role of protein: hosts haem, stop oxidation of iron to ferric form, provides pocket for oxygen binding

Question 8

Explain how the structure of myoglobin reduces the risk of carbon monoxide poisoning.

Answer 8

• Carbon monoxide: binds strongly to free haem (poison) (∵ very strong dative linear bonds between Fe and C)
• Distal histidine forces a bend (∵ steric hindrance tilts the bond to destabilise the interaction between Fe and C) -> weakens Fe-CO complex to reduce stability
• ∴ Myoglobin binds CO less strongly than free haem (but still can poison)

Question 9

Explain what is a oxygen dissociation curve and define pO2(torr) and p50 value. What is the unit for oxygen-binding site in myoglobin?

Answer 9

• Oxygen dissociation curve: measure affinity of O2
• pO2(torr): partial pressure of O2 (∝ [O2])
• p50 value: [O2]/pO2 needed to saturate 50% of myoglobin haem
• 1 haem = 1 oxygen-binding site