L11: Protein Folding Flashcards
(42 cards)
What stabilises folded proteins?
Stabilised by a mixture of non-covalent & covalent interactions
- Hydrogen bonds
- Electrostatic interactions
- London forces
- Hydrophobic effect
- Disulphide bonds
Typical contributions of non-covalent interactions
Dispersion interaction
Electrostatic interaction
Hydrogen bonding
Hydrophobic interactions
Structure of H2O
2 H+ atoms in each molecule
2 lone pairs on each O2
=
Which individual H2O molecule contribute to 2 H+ bonds a donor
2H+ bonds as an acceptor
Why is water important in protein folding?
It influences hydrophobic & hydrophilic interactions
2 solvation effects
1) Hydrophobic ‘interaction’
Hydrophilic interactions
What are hydrophobic solvation effects? and what is the folding impact?
H2O can’t form H bonds with hydrophobic groups
- Instead, form cages around them to reduce entropy
Folding impact: Burial of hydrophobic residues inside protein
What is the hydrophilic solvation effects? and what is the folding impact?
Favourable interactions with polar/charged groups that lowers energy
Folding impact: Exposure of hydrophilic residues on surface
Which type of interactions stabilize protein tertiary structure?
Hydrophobic interactions
How many residues are present in the example human lysozyme discussed in the lecture?
129 residues
What is entropy?
Disorders/randomness of a system
What is the entropy of folding?
Difference between the entropy of the native state & the unfolded state
Why does unfolded proteins have higher entropy?
Due to numerous conformational states
Proteins are marginally stable but what can it be easily denatured by?
1) Temp changes
2) pH variations
3) Mutations
Key experimental findings in protein folding
1) Spontaneous process
2) Fast process
3) Co-operative
4) Thermodynamics suggest a free energy for folding around
How many possible conformations in a 100-reside protein?
10^100
What is Levinthal’s Paradox?
If proteins folded randomly, it would take 10^80 years to find the correct fold
SO
Proteins follow specific folding pathways via energy landscapes
What did Anfinsen’s Experiment (1961) show?
Protein structure is encoded in its amino acid sequence
Ribonuclease A unfolded in urea & mercaptoethanol but refolded to its native structure upon removal of denaturants
What does disulfide bond formation stabilise?
Folding intermediates
Folding pathway of lysozyme
What does early intermediates contain?
alpha-helices, while beta-sheets form later
What happens to hydrophobic residues during protein folding?
Hydrophobic residues are buried in the interior of the protein
What type of bonds are formed during the folding of proteins like bovine pancreatic ribonuclease?
Disulfide bonds
What is the estimated time it takes for proteins to fold based on experimental findings?
1 second
Discuss the importance of the hydrophobic effect in protein folding.
The hydrophobic effect is crucial in protein folding because it drives nonpolar amino acids to the interior of the protein, away from water. This process stabilizes the protein’s structure, allowing it to achieve its functional shape and maintain biological activity.
What does Anfinsen’s experiment illustrate about protein folding?
The amino acid sequence determines the protein’s three-dimensional structure
