L11: Protein Folding Flashcards
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 is the hydrophobic solvation effects?
Removing hydrophobic resides from the water-protein interface is entropically favourable
What is the hydrophilic solvation effects?
Interactions between H2O and hydrophilic resides are enthalpically favourable due to potential hydrogen bonding & charge interactions
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?
Related to the no. of states (degrees of freedoms) a molecule can adopt
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
Which experiment demonstrated that amino acid sequences encode protein structure?
The Anfinsen experiment
What is the relationship between solvation effects and protein folding?
Solvation effects stabilize the folded state of proteins
What role do chaperones play in protein folding?
Chaperones assist in proper protein folding
What types of non-covalent interactions contribute to protein stability?
Hydrogen bonds, ionic interactions, van der Waals forces, and hydrophobic interactions
What is the relationship between solvent exclusion and protein stability?
Solvent exclusion enhances protein stability by promoting proper folding
How does water influence the folding process of proteins?
Water stabilizes protein folding through hydrophilic and hydrophobic interactions
Function of chaperones
Prevents aggregation
Assist in protein folding
Help transport proteins across membranes
How does the amino acid sequence influence the final folded structure of a protein?
The amino acid sequence determines how a protein folds by influencing interactions like hydrogen bonds, ionic bonds, and hydrophobic effects.
These interactions guide the protein into its specific three-dimensional shape, which is crucial for its function.
The amino acid sequence determines how a protein folds by influencing interactions like hydrogen bonds, ionic bonds, and hydrophobic effects. These interactions guide the protein into its specific three-dimensional shape, which is crucial for its function.
Chaperone proteins
Presence of disulfide bonds
Amino acid sequence
Describe the closed state of GroEl/S chaperone
Hydrophobic regions exposed which binds unfolded proteins
Describe the open state of GroEl/S chaperone
Hydrophilic regions exposed which allows protein folding
What disease is caused by a single mutation of Glu to Val?
Sickle cell anaemia
Effect of mutation of Glu to Val
Val interacts with hydrophobic pockets, forming fibers that distort red blood cells
What is the significance of β-sheet formation in protein aggregation?
β-sheet formation contributes to the stability of protein aggregates
Alzheimer’s Disease
Amyloid-beta peptide misfolds into beta-sheet aggregates, forming plaques in the prain
Prion Diseases
PrP protein misfolds into an infectious beta-sheet-rich form (PrPSc)
PrPSc induces other PrP proteins to misfold, forming aggregates
What does misfolded proteins aggregate via beta-sheet interactions form?
Amyloid fibrils (Alzheimers)
Neurofibrillary tangles (Parkinsons)
What is protein folding driven by?
Thermodynamics, with a balance of enthalpy & entropy
