Part 1: Protein folding

Question 1

Unfolded proteins can form:

Answer 1

• aggregates that interfere with other cellular functions.
  
  • Increased levels of misfolded proteins can lead to neurodegenerative conditions

Question 2

Chaperones do not enhance correct folding. Rather they:

Answer 2

• prevent non-productive routes

Question 3

Principle of minimal frustration posits:

Answer 3

• evolution has selected polypeptide chains in which the individual amino acids are positioned so that they maximize correct folding events, and minimize structural barriers (through their side chains).

Question 4

Does the folding pathway for a polypeptide chain proceed in a linear manner, whereby lower and lower free energy states are achieved?

Answer 4

• No
• local thermodynamic minima can arise that have to be overcome to continue down the folding pathway. The occurrence of local energy minima can lead to ‘kinetic traps’ that lock the nascent polypeptide chain in a non-productive conformation.

Question 5

What type of interactions promote folding?

Answer 5

1. hydrophobic core
2. electrostatic interactions
3. van der Waals interactions
4. disulfide bonds
5. metal coordination

Question 6

The formation of a hydrophobic core involves:

Answer 6

• collapse of hydrophobic side-chains into the interior of the nascent folded protein so that contact with water molecules is minimized.

Question 7

Is protein denaturation reversible?

Answer 7

• yes, for some small, single domain proteins
• no, for large, multi-domain proteins

Question 8

What agents can promote protein unfolding?

Answer 8

1. Temperature
2. pH
3. pressure
4. urea
5. guanidine
6. organic solvents

Question 9

What agents promote protein folding?

Answer 9

1. co-factors (heme; folate; B6; B12)
2. disulfide bonds
3. chaperones
4. physiological partners

Question 10

What is the general role of chaperones?

Answer 10

• stabilize the nascent chain (just exited ribosome)
• prevent deleterious interactions with other constituents in the cell
• provide an opportunity for the protein to achieve its mature structure

Question 11

The continuum model posits that:

Answer 11

• a polypeptide chain can enter multiple folding pathways, although only one path leads to a productive native structure.
• predicts that a ‘folding funnel’ can explain the mechanism.

Question 12

A molten globule is:

Answer 12

• a polypeptide chain that:
  
  • is near-final secondary structure
  • is ‘looser’ and more ‘open’ than the final structure
  • has domains trying out and searching for lowest energy state

Question 13

Is a molten globule a single structure?

Answer 13

• No.
  
  • it is a collection of similar intermediates

Question 14

What is the driving force of molten globules?

Answer 14

• water exclusion

Question 15

Process of the ‘water exclusion’ driving force:

Answer 15

• hydrophobic side chains interacting with water drive folding to place them into the core of the protein with other hydrophobic residues
• simultaneously, water is pushed out of protein core

Question 16

What is the role of chaperones chaperones in multi-domain proteins?

Answer 16

• maintain individual domains in a loosely assembled state to enable final interactions with other domains that are not yet synthesized

Question 17

What are the three models of protein folding?

Answer 17

1. Hierarchical
2. Nucleation-Condensation
3. Hydrophobic Collapse

Question 18

Hierarchical model of protein folding:

Answer 18

• secondary structures come first, and then through intramolecular interactions promotes the assembly of the tertiary structure.

Question 19

Nucleation-Condensation model of protein folding:

Answer 19

• secondary and tertiary structures of the protein are made at the same time
• results in rapid propagation of the structure motif, which coalesce and stabilize the final native structure

Question 20

Hydrophobic collapse model of protein folding:

Answer 20

• a molten globule forms as a result of tertiary hydrophobic interactions
  
  • initiates secondary structure maturation and the final tertiary structure

Question 21

Do chaperones increase the rate of protein folding?

Answer 21

• No - they improve the yield of successfully folded products

Question 22

What are the key features of a chaperone?

Answer 22

• may or may not require energy
• do not remain associated with their target
• do not increase the rate of folding
• increase the yield of properly folded products

Question 23

What type of proteins can refold after full denaturation?

Answer 23

• single domain proteins
  
  • All the key structural information is available in the sequence.

Question 24

The major consumption of cellular energy occurs during:

Answer 24

• protein synthesis
  
  • therefore, repair is first attempted for misfolded proteins rather than degradation

Question 25

Bacterial GroEL chaperone structure and function:

Answer 25

• multi-subunit cylindrical particle (four rings)
• large hydrophobic cavities present at both ends of the cylinder (can bind unfolded proteins here)
• attempts to refold damaged/misfolded proteins

Question 26

Bacterial GroEL chaperone mechanism of refolding damaged proteins:

Answer 26

• uses the energy of ATP hydrolysis to exert mechanical force into the unfolded protein
• structural changes in GroEL caused by ATP hydrolysis are believed to shield hydrophobic residues, and instead expose hydrophilic residues in the wall of the cavity. This might force the hydrophobic residues in the unfolded protein to become buried, thereby assuming proper structure.