Protein Folding

Question 1

What is cumulative selection?

Answer 1

The tendency to retain partially correct intermediates bc they are slightly more stable than unfolded regions

Question 2

what is protein disulfide isomerase?

Answer 2

catalyzes the interchange of disulfide bonds until the bonds of the native conformation are formed; also plays a role in the elimination of folding intermediates with improper disulfides

Question 3

what is peptide prolyl cis-trans isomerase?

Answer 3

catalyzes the interconversion of cis/trans isomers of pro peptide bonds

Question 4

To represent a viable form of secondary structure the folding pattern must:

1) Optimize the hydrogen bonding potential of the main-chain carbonyl and amide groups.
2) Represent a favored conformation of the polypeptide chain.

Answer 4

ya

Question 5

constraints on a helices

Answer 5

1) Electrostatic repulsion (or attraction) between successive residues with charged R groups.
2) The bulkiness of adjascent R groups.
3) The interactions between residues spaced by three or four residues.
4) The occurrence of Proline and Glycine.
5) The interaction between amino acids at each end of the helix and the helix dipole.

Question 6

what is a motif?

Answer 6

(aka folds, aka super-secondary structure) are recognizable folding patterns involving two or more elements of secondary structure and the
connections between them.

Question 7

what are domains?

Answer 7

part of a polypeptide chain that are independently stable or can undergo movements as a single entity with respect to the entire protein

Question 8

Motifs can represent small, simple patterns such a β-α-β loop or very elaborate structures like β-Barrels.
• A single large motif, such as the β-Barrel, may comprise the entirety of the protein.
• Motifs may or may not be independently stable.
• Motifs are not heirarchial structures between secondary and tertiary structure, rather they are simply a folding pattern.

Answer 8

ya

Question 9

Types of folds or motifs we’d expect to see:
• H bonding and allowing conformation are the rules to form elements of secondary structure
• Types of motifs we’d see (super secondary structures)–>based on the same rules
○ An amphipathic beta sheet will bond with another with the extension of the rule: hydrophobic bonding
§ “sandwich effect”
○ 10:39–alpha and beta can’t come together?
§ Can’t have a mix of both to match H bonds

Answer 9

ya