Professional Documents
Culture Documents
Van Vranken
H
[O]
Van Vranken
1. The drug captopril is an inhibitor of angiotensin I-converting enzyme. Access the crystal structure of
human testicular angiotensin I-converting enzyme bound to captopril (PDB code: 1UZF). When you
look at the introductory page you can see that the ligand is abbreviated as MCO in the structure.
-O
-O
SH
captopril
N
captopril
+
enzyme
S
X
Zn X
X
?
Right click with the mouse on the protein display window and click console
Select all
Cartoon off
Spacefill off
Wireframe off
Select zinc or MCO
Wireframe 0.3
Select within(7, zinc)
Wireframe
Select within(7, zinc) and *.ca
Label %m%r
Select all
wireframe off
Select MCO or 383 or 387 or 411 or zinc
Wireframe 0.3
Color cpk
Select zinc
Spacefill
Select protein
Select mco
Dots
Select all
Rockets
-O
H387
S
Zn N
N
O
H383
Van Vranken
N
H
NH
O
E411
2. Several commercial biocides were tested for lethality against aquatic plants in both fresh
water (FW) and salt water (SW).1
a. Estimate the 50% lethal dose (LD50) for Diuron against saltwater plants.
b. Which biocide the most safe to freshwater (FW) aquatic plants?
all of them
are >99% lethal
above 10,000 g/L
Diuron-SW
40 g/L
(an estimate is OK)
3. Using structures in the protein databank, correctly match the protein domains with the
proteins that contain them.
Protein Databank code
3EMH
2NZI
1XIO
3FYL
3GU4
Protein Domain
Seven-transmembrane domain
kinase
Zinc finger
WD40
Fibronectin FNIII
Van Vranken
Answer
Protein Databank code
3EMH
2NZI
1XIO
3FYL
3GU4
Protein Domain
WD40
Fibronectin FNIII and Ig domains
Seven-transmembrane domain
Zinc finger
kinase
Gln81
Arg86
H
H
H
Arg57
H
N
N
N
N H
N H
H
O
H
O
O P O
O
H N
O
HO
H
OH
OOH
H
5. A monoclonal antibody against nitrotyrosine residues has been created for use in ELISA
assays.2 In order to test the specificity of the antibody, a variety of tyrosine deriveatives were
tested for their ability to competitively INHIBIT binding of the anti-nitrotyrosine antibody to the
nitrotyrosines on the surface of the ELISA well.
4
Van Vranken
competitive inhibitors
X
HO
X
OH
HO
X
HO
OH
antibody
X
X
HO
X
HO
R
R
HO
NO 2
O2N
HO
NO 2
OH
HO
NO 2
HO
NO 2
HO
NO 2
c. The protein bovine serum albumin (BSA), an inexpensive protein from cow blood, was
nitrated such that each protein had three to six nitrotyrosine residues per protein. What
percentage of the tyrosines in BSA were modified in the nitration reaction.
SQ
SEQUENCE
MKWVTFISLL
DEHVKLVNEL
ERNECFLSHK
ANKYNGVFQE
FSQYLQQCPF
MADCCEKQEP
YFYAPELLYY
ERALKAWSVA
FVEVTKLVTD
HCIAEVEKDA
RLAKEYEATL
IVRYTRKVPQ
PVSEKVTKCC
ALVELLKHKP
Van Vranken
LTKVHKECCH
IPENLPPLTA
EECCAKDDPH
VSTPTLVEVS
TESLVNRRPC
KATEEQLKTV
GDLLECADDR
DFAEDKDVCK
ACYSTVFDKL
RSLGKVGTRC
FSALTPDETY
MENFVAFVDK
ADLAKYICDN
NYQEAKDAFL
KHLVDEPQNL
CTKPESERMP
VPKAFDEKLF
CCAADDKEAC
QDTISSKLKE
GSFLYEYSRR
IKQNCDQFEK
CTEDYLSLIL
TFHADICTLP
FAVEGPKLVV
Answers:
a.
HO
NO 2
HO
Cl
HO
O-
3N
3-nitrotyrosine
NO 2
+H
O-
3N
H
N
H 2N
O
3-chlorotyrosine
O
N
H
H
N
O-
GlyGlyTyr(NO 2)Arg
NH
+H
2N
-6
NH 2
Th. Caquet, M. Roucaute, N. Mazzella, F. Delmas, C. Madigou, E. Farcy, Th. Burgeot, J.-P.
Allenou, R. Gabellec Risk assessment of herbicides and booster biocides along estuarine
continuums in the Bay of Vilaine area (Brittany, France) Environmental Science and Pollution
Research 2013, 20, 651-66.
2
Jamshad KHAN, David M. BRENNAN, Nicholas BRADLEY, Beirong GAO, Richard
BRUCKDORFER, Michael JACOBS 3-Nitrotyrosine in the proteins of human plasma
determined by an ELISA method Biochem. J. 1998, 330,795801.