Problem Set 2 KEY
Question 1
The PDB file for Ca2+-bound calmodulin (PDB code 1EXR) was determined from a
crystal with unit cell dimensions a = 25.0
... [Show More] Å, b = 29.4 Å, and c = 52.8 Å. The X-ray
source had a wavelength of 0.886 Å. Considering only diffraction planes parallel with
the b-c plane, i.e. Miller indices (h 0 0), give the diffraction angle for the first and second
order reflections.
Bragg’s Law: 2 d sinθ = nλ
The spacing between diffraction planes is equal to the unit cell dimension a = 25.0
Å.
For the first order reflection: 2 × 25.0 sinθ = 1 × 0.886 and therefore θ = 1.02°
For the second order reflection: 2 × 25.0 sinθ = 2 × 0.886 and therefore θ = 2.03°
The diffraction angles (diffraction angle = 2θ) are 2.04° and 4.06°.
Question 2
F0F1-ATPase is an incredible enzyme in the inner membrane of the mitochondrion,
composed of a transmembrane proton channel (F0) which acts as a generator to drive
ATP synthesis by an associated F1 motor complex. The crystal structure of the purified
F1 motor is shown below:
α subunit
β subunit
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2
a) What kind of symmetry does the F1 motor have?
Three-fold cyclic symmetry (C3). (It also has pseudo-C6 symmetry, but the α and
β subunits are slightly different.)
b) In the lab, you purify the F1 protein from a newly discovered species. Based on
calculations made by a website server, the extinction coefficient at 280 nm is ε = 29,000
M-1 cm-1 for the α subunit and ε = 44,000 M-1 cm-1 for the β subunit. What is the
extinction coefficient for F1-ATPase?
Absorbance is additive, therefore the combined extinction coefficient for F1-
ATPase is: ε = 3 × εalpha + 3 × εbeta = 3 × 29,000 + 3 × 44,000 = 219,000 M-1 cm-1.
c) Your purified sample of F1-ATPase absorbs 94% of incident light at 280 nm using a
standard 1 cm path length cuvette. What is the concentration in micromolar?
Beer’s Law: A = log10 (I0/I) = ε c l
Therefore… log10 (1 / (1 – 0.94)) = 219,000 × c × 1
And concentration = 5.6 × 10–6 M or 5.6 µM.
Question 3
In humans, the protein Bax is a tumor suppressor that initiates programmed cell death.
Bax functions by binding and inhibiting a pro-survival protein called Bcl-2. Bax binds
Bcl-2 via a short helical segment with sequence KKLSECLKRIGDELDSNM.
a) Write out Bax sequence KKLSECLKRIGDELDSNM in the helical wheel diagram
below. Does this helix have a hydrophobic moment? If so, indicate the direction of the
hydrophobic moment with an arrow [Show Less]