Chem 128 Introduction to Chemical Biology

Van Vranken

Problem Set 8 - Key

1. a. Protein kinase D is activated by phosphorylation of two serine residues in the activation
loop: ALSERVSIL. Draw the chemical structure of the activation loop of protein kinase D in
the phosphorylated form as an extended peptide backbone in a zig-zag conformation.
b. The serine residues can be mutated to another type of residue, resulting in a mutant form of
protein kinase D that is always activated. Which other amino acid mimics the shape and
charge of phosphoserine?
Answer:
S744E/S748E double mutation leads to constitutive activation of protein kinase D.
+
HN

ALSERVSIL

N
H

H
N

O
N
H

HO
OO P
O
H
N

NH 2
NH

O
N
H

O
O

H
N
O

ALEERVEIL

N
H

H
N
O

O-

O
N
H

N
H

NH 2
NH

H
N

O+
HN

HO
OO P
O
O
H
N
N
H
O

N
H

O
O

H
N
O

O-

O
N
H

H
N
O

O
N
H

O-

Cantrell, D. A. Transgenic analysis of thymocyte signal transduction Nature Reviews

Immunology 2002, 2, 20-27.
Waldron, R. T. et al. Activation loop Ser744 and Ser748 in protein kinase D are
transphosphorylated in vivo. J. Biol. Chem. 2001, 276, 3260632615.
2. a. Dust mites that live off of the dead skin that comes off of your
body. They express a cysteine protease called Der p1 protease that
cleaves human proteins. Draw a structure of the covalent adduct that is
temporarily formed between the target protein and the Der P1 protease
enzyme.

Chem 128 Introduction to Chemical Biology

Van Vranken

b. Some people have an allergic reaction to their own proteins once they are cleaved by dust
mite Der p1 protease. A synthetic molecule has been designed as an irreversible inhibitor that
binds covalently to Der P1 protease. Draw a plausible chemical structure for the stable
covalent adduct that forms between the inhibitor and Der p1 protease.
Der p1

N
H

H
N

H
N

N
H

Der p1

-S

H
N

N
H

N
H

H
N

-S

O
N
H

H
N

O
O

synthetic
Der p1 protease inhibitor

human protein
NH 3+

NH 3+

Answer:
Der p1

N
H

H
N

H
N

N
H

O Der p1

N
H

Der p1protein
intermediate

H
N
O

O
N
H

H
N

O
O

covalent adduct

NH 3+

NH 3+

Harris J, Mason DE, Li J, Burdick KW, Backes BJ, Chen T, Shipway A, Van Heeke G, Gough
L, Ghaemmaghami A, Shakib F, Debaene F, Winssinger N. Activity profile of dust mite
allergen extract using substrate libraries and functional proteomic microarrays. Chem Biol.
2004, 11, 1361-72.
3. Draw the structure for Gal1-3Gal1-3Xyl-O-Serine with each of the monosaccharide
subunits in a chair conformation with clearly defined axial and equatorial substituents.
Answer:
Gal
OH
HO
HO

HO
O

OH

Gal
OH
O HO
O
H
OH

Xyl

-O
O

OH

Gal1-3Gal1-3Xyl-O-Serine

NH 3+

4. Draw the structure of human type I LN2 antigen using compact notation (e.g., Glc14GalNAc1-2Glca-OR).

Chem 128 Introduction to Chemical Biology

HO

OH

OH
O H
OO
OH

HO

HO

OH

OH
O H
OO
HO

O
NHAc

Van Vranken

HO

OH
O

O
NHAc

OR

HO

Answer:
Gal1-3GlcNAc1-3Gal1-3GlcNAc-OR

HO

OH

OH
O H
OO
OH

HO

HO
O

O
NHAc

GlcNAc

Gal

OH

OH
O H
OO

HO
Gal

HO

OH
O

O
NHAc

GlcNAc

HO

OR

Gal

5. Draw the structure of the following branched glycan using compact notation (e.g., Glc14GalNAc1-2Glc-OR).
HO

OH

OH
O

HO

O
O
HO

O
O
OH

OH

OH

HO

OH
O

O
NHAc
OH

OR

HO

OH

Answer:
HO

Gal
OH
O

HO

O
O
OH

OH O

O
O

HO

GlcNAc
OH

OH
Fuc

Fuc

Gal
OH
HO

O
O
NHAc
OH

O
HO

OR

Fuc1-2Gal1-4
GlcNAc1-3Gal-OR
Fuc1-3

OH

6. Highlight each of the 2-carbon units derived from acetate and the 3-carbon units derived
from propionate in the polyketide natural products below. Note that the initial starter unit may
be contain more than 3 carbons.

Chem 128 Introduction to Chemical Biology

OH O

Van Vranken

ebelalactone A
O

OH OH OH O

BE-14106

O
NH

OH

OH

HO

O
OH

HO

OH OH

OH

OH

terefibricin I

HO

NH 2

OH

OH
O

roxaticin

tedanolide

HO

OH
O

OH OH OH OH OH

OH O

OH O

Answer:
It is usually best to start from
the carboxylic acid end

ebelalactone A
OH O

O
O

OH OH OH O

BE-14106

NH

OH

OH

HO

O
OH

HO

OH OH

OH

OH

terefibricin I

HO

NH 2
???

OH

OH
O

roxaticin

tedanolide

OH
O

HO
O

OH OH OH OH OH

OH O

OH O