Homework 4 BCH2333 Winter 2017

Topics covered: Primary and secondary, motifs

1. a) Highlight the nonpolar residues in the sequence below. Y and T can be nonpolar or polar in
this case I have called them nonpolar since it fits the pattern of alternating nonpolar residues.

NYKTRAEVKFEGPTLNVRIELKG

b) Is there a potential turn in this sequence? If so, highlight the residues involved in the turn. GP
is the turn.

c) Fit this sequence on to a -hairpin motif (use the anti-parallelt -sheet model from the notes)
and an -hairpin motif (used the helical wheel/coiled-coil diagram). Which is a better fit?

Beta-hairpin

Gly Pro

R H R
Top face N
Bottom HN O O Top face
face O H N
Glu R R Thr
N H OBottom
O NH face
Phe R R Leu
HN O
O H N
Lys R R Asn
N H O
O NH
Val R R Val
HN O
O H N
Glu R R Arg
N H O
O NH
Ala Ile
HN O
O H N
Arg Glu
N H O
O NH
Thr Leu
HN O
O H N
Lys Lys
N H O
O NH
Tyr Gly
HN O
O H N
Asn
N H O
O NH

HN O

Top face is charged and polar, bottom face is non-polar.

Good fit.
Homework 4 BCH2333 Winter 2017

Helical wheel alpha hairpin

Poor fit. No obvious nonpolar faces to bind to form the alpha-hairpin

d) What do you notice about the pattern of where the nonpolar residues occur? Does this make
sense based on the best fit model from above? Alternating nonpolar and polar residues. This
fits the beta-sheet model since it makes one face of the helix nonpolar and the other charged.

2. a) highlight the nonpolar residues in this sequence

NLEEAFEHLASPGAVSNIETMANSL

b) Are there potential turns in this sequence? If so, where? PG is a turn.

c) Fit this sequence on to a -hairpin motif (use the antiparallelt -sheet model from the notes)
and an -hairpin motif (used the helical wheel/coiled-coil diagram). Which is a better fit?
Homework 4 BCH2333 Winter 2017

Beta-hairpin

Pro Gly

R H R
Top face N
Bottom HN O O Top face
face O H N
Ser R R Ala
N H O Bottom
O NH face
Ala R R Val
HN O
O H N
Leu R R Ser
N H O
O NH
His R R Asn
HN O
O H N
Glu R R Ile
N H O
O NH
Phe Glu
HN O
O H N
Ala Thr
N H O
O NH
Glu Met
HN O
O H N
Glu Ala
N H O
O NH
Leu Asn
HN O
O H N
Asn Sel
N H O
O NH
Leu
HN O

Not an amphipathic beta-sheet

Homework 4 BCH2333 Winter 2017

Helical wheel diagram for alpha-hairpin

Good fit.

d) What do you notice about the pattern of where the nonpolar residues occur? Does this make
sense based on the best fit model from above? Nonpolar residues as I, i+3, i+4, i+7 etc. This
fits to an amphipathic helix model extremely well.

3. a) highlight the nonpolar residues in this sequence.

TIWVYGTPEELKKLKEEAKKGNIRVTF

b) Are there potential turns in the sequence? If so, where? Two the P and the G at residue 21

c) What motif does this likely correspond to? Beta-alpha-beta.

4. Use two helical wheel diagrams to display the dimerization region of CREB. The CREB leucine zipper
region has the following sequence (one-letter code)

LENRVAVLENQNKTLIEELKALKDLY

Show the hydrophobic interface and identify three additional favorable interactions at the dimer
interface.
Homework 4 BCH2333 Winter 2017

H-bond between the Ns at 5 and e, stalk briges between the Rs and Es at 4 and d, H bonding between
the Qs at 4 and d.