lecture 19 - protein structure: loops & turns

Question 1

explain what loops and turns do

Answer 1

connect secondary structure elements

Question 2

do loops and turns have repetitive phi/psi angles?

Answer 2

no

Question 3

are loops flexible? why or why not?

Answer 3

• yes

- lack regular h-bonding patterns

Question 4

for a parallel beta sheet, loops can be:

Answer 4

short or long

Question 5

for an antiparallel beta sheet, loops can be:

Answer 5

• short only
• usually 4 amino acid residues
• compact and well ordered
• allows 180° redirection of the backbone
• positions 2/3 are often Gly or Pro
• gly is small - allows phi/psi angles needed for tight turn
• pro forces a kink in the backbone (helix/sheet breaker)

Question 6

define motif & what is it used for?

Answer 6

• pattern formed by 2 or more 2° structure elements and the connections between them
• not necessarily functional
• used to build up 3° structure (3D fold)

Question 7

what stabilizes a motif?

Answer 7

• stabilized by H-bond within helix and between b-sheets
• stabilized by R-group interactions between helix & B-sheet (typically hydrophobic)
• possibly electrostatic reactions

Question 8

can you build a 3D fold with multiple motifs?

Answer 8

yes

Question 9

describe a beta/alpha barrel

Answer 9

• beta-sheet connected to alpha helix, connected to beta-sheet, etc.
• wraps into cylindrical fold
• B-strands inside
• alpha-helices outside
• many structures have this fold (enzymes, membrane pores) - all with diverse functions