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Circular Dicroism
Fluorescence
Instrumentation
Methods for Secondary Structural Analysis
• A number of experimental techniques can selectively
examine certain general aspects of macromolecular • The most common instruments around are the
structure with relatively little investment of time and currently produced JASCO, JobinYvon, OLIS,
sample. and AVIV models.
• Reasonable estimates of protein secondary structure
content and structure change can be determined • We have the Jasco 710 and 810 models with
empirically through the use of temperature controllers. The air cooled 150W
Circular dichroism (CD) spectroscopy Xenon lamp does not necessitate water cooling.
Fluorescence spectroscopy • You still need to purge with ample nitrogen to get
Nuclear Magnetic Resonance (NMR) spectroscopy to lower wavelengths (below 190 nm).
FT-infrared spectroscopy
1
Sample Preparation and Measurement
• Additives, buffers and stabilizing compounds: Any compound,
which absorbs in the region of interest, (250 - 190 nm) should be CD Data Analysis
avoided. A buffer or detergent, imidazole or other chemical should
not be used unless it can be shown that the compound in question • The molar ellipticity [] is related to the difference in
will not mask the protein signal.
• Protein solution: The protein solution should contain only those extinction coefficients
chemicals necessary to maintain protein stability/solubility, and at [] = 3298 Δε.
the lowest concentrations possible. The protein itself should be as
pure as possible, any additional protein will contribute to the CD • Here [] has the standard units of degrees cm2 dmol -1
signal.
• Contaminants: Particulate matter (scattering particles), anything • The molar ellipticity has the units degrees deciliters
that adds significant noise (or artificial signal contributions) to the mol-1 decimeter-1.
CD spectrum must be avoided. Filtering of the solutions (0.02 m
syringe filters) may improve signal to noise ratio.
• Data collection: Initial experiments are useful to establish the best
conditions for the "real" experiment. Cells of 0.5 - 1.0 mm path
length offer a good starting point.
CD Signal of Proteins
CD Data Analysis • For proteins we will be mainly concerned with absorption
• To be able to compare these ellipticity values we need to in the ultraviolet region of the spectrum from the peptide
convert into a normalized value. The unit most commonly bonds (symmetric chromophores) and amino acid
used in protein and peptide work is the mean molar sidechains in proteins.
ellipticity per residue. We need to consider path length l, • Protein chromophores can be divided into three classes: the
concentration c, molecular weight M and the number of peptide bond, the amino acid sidechains, and any
residues. prosthetic groups.
in proper units (CD spectroscopists use decimol) • The lowest energy transition in the peptide chromophore is
an n → p* transition observed at 210 - 220 nm with very
which finally reduces to weak intensity (emax~100).
2
Protein CD Signal
• The three aromatic side chains that occur in proteins (phenyl
group of Phe, phenolic group of Tyr, and indole group of
Trp) also have absorption bands in the ultraviolet spectrum.
However, in proteins, the contributions to the CD spectra in
the far UV (where secondary structural information is
located) is usually negligible. Aromatic residues, if
unusually abundant, can have significant effects on the CD
spectra in the region < 230 nm, complicating analysis.
• The disulfide group is an inherently asymmetric
chromophore as it prefers a gauche conformation with a
broad CD absorption around 250 nm.
Comparison of the
UV absorbance
(left) and the
Far UV CD Spectra of Proteins
circular dichroism
(right) of poly-L-
[] x10-3 degrees cm2 dmol -1
lysine in different
secondary structure
conformations as a
function of pH.
3
CD Spectra Fit Conformational Change of CD2
c
• In a first approximation, a CD spectrum of a protein or
polypeptide can be treated as a sum of three components: 0
25 ºC
(1)
-2000
• θT is the total measured ellipticity, θh the contribution from
helix, θs for sheet, θc for coil, and the corresponding χ the 85 ºC
fraction of this contribution.
-3000
200 210 220 230 240 250 260
Wavelength (nm)
Wavelength (nm)
75 m3 65.718 0.11006
10 85
-4 m4 2.644 0.095431
95
CD, mdeg
Chisq 2.7395 NA
R 0.99849 NA
5 -5
B
-6
0
-7
Tm = 65.7 °C
-5
-8
-10 -9
200 210 220 230 240 250 260 0 20 40 60 80 100
Wavelength, nm Temperature, C
4
Fluorescence measurement
Trp
c
a folded protein), Trp
25ºC
emission occurs at
shorter wavelength.
Fluorescence intensity
4
3 10
hvem
85ºC
solvent, its emission is
vex > vem 1 10 4
5
Summary of fluorescence
• Fluorescence is the emission of radiation that occurs when a
molecule in an excited electronic state returns to the ground state.
• Application: Fluorescence has an important role in the structural
determinants of proteins, DNA or RNA, etc.
• Advantages:
– Small sample volumes (800μL – 3mL)
– Low concentration (0.1 – 5 M)
– Short experiment time (10-60 minute)
– Short data analysis time (5-30 minute)
– Recovery of sample
• Disadvantages:
– Large Stoke’s Shift
– Background fluorescence (Impurities in buffers and
autofluorescence in cells)
– Scattered light (problem with cloudy samples)