Exploring the Model
Step2
Tape together the strips
so that the lowercase letter
on the white background
(e.g., a) is taped on top of
the same letter on the
shaded background. Repeat
this for letters b through k
to create a long strip.
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Next tape strand C next to B, D next to C and
so on till strand K, in each case aligning the grey
areas between the strands and making sure the
arrows in these strands point up and down
alternately as shown in the diagram on the right.
At the end of this step the beta sheet should
have strands labeled A-K reading from
left to right.
At this point make sure the chromophore
strip is behind the printed side
of the beta sheet.
GFP is a protein that can exhibit light. It is widely used in biotechnology.
The GFP model was created using
data from the PDB archive
PDB ID: 1EMA
M. Ormo, A. B. Cubitt, K. Kallio, L. A. Gross,
R. Y. Tsien, S. J. Remington (1996)
Crystal structure of the Aequorea victoria
green fluorescent protein.
Science 273: 1392-1395
Lay the strand labeled A on
the table so that the arrow is
pointing upwards, place
strand B to the right of A and
orient it so that the arrow
points to the bottom. Align
the grey areas between the
strands (representing the
hydrogen bonds between
them), and tape top to bottom
on the aligned grey area.
*
Close the GFP beta barrel
by aligning the grey area
between strands A and K
and taping them together.
The chromophore should be
inside the barrel.
1. Can you trace the polymer chain from the
amino to carboxy terminus? Hint: the order
of the strands from amino to carboxy
terminal are marked with the numbers 1-11
(in the arrowheads of each strand).
2. What is the relationship between the strand
labels A-K and 1-11? Comment also on the
loops between the strands and location of
the chromophore.
3. Identify one example each of parallel and
antiparallel strands in the GFP barrel.
Step 3 Step 4
The Primary Structure
The long strip of paper from
amino (NH3+) to carboxy
(COO-) represents the
primary structure of GFP.
Regions of secondary structure
(beta strands and alpha
helices) are marked.
&
To learn more, read the
Molecule of the Month feature on (GFP) at
dx.doi.org/10.2210/rcsb_pdb/mom_2003_6strand number
1
align
&
tape
Paper Model of Green Fluorescent Protein (GFP)
Cut out the 12 strips of
paper (outlined in dotted
line) representing the 11
beta strands and 1 helical
region of the GFP.
Step1
0.8035 in0.8035 in
A
B
C
D
E
F
G
H
I
J
K
alternate the arrows
Step 5
move the chromophore strip
from the front (shown)
to the back of the printed side
align
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chromophore
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Paper Model of Green Fluorescent Protein (GFP)
K