Circular Dichroism and
Optical Rotary Dispersion
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Applications
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- Protein/Peptide conformation studies.
- Thermal and chemical denaturation studies.
- Structural determination
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Instrument
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Date Installed
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Detection Capabilities
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- Circular Dichroism
- Optical Rotary Dispersion
- Emission Fluorescence (full spectrum excitation & emission bandwidth)
- Ultraviolet and Visible Wavelengths.
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Sample Holders
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- Peltier thermostated for temperature melts in only rectangular cells.
- Room temperature for cylindrical or rectangular cells.
- Constant temperature (water bath controlled) for only cylindrical cells.
- Constant temperature (water bath controlled) for only rectangular cells.
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Typical Sample
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Far UV-CD (α-helix, β-structures)
- 0.3 ml of a 0.5 OD in a 1 mm rectangular cell.
- Peptide or protein: 0.3 ml of a 0.1 mg/ml sample in a 1 mm rectangular cell.
- This is 40 uµg of protein or peptide.
Near UV-CD (Aromatic amino acid environment)
- 2.0 ml of 1.0 mg/ml protein.
- 1-cm cell
- This is 2 mg of protein or peptide.
If concentration is a concern and your protein or peptide cannot be analyzed
at these concentrations, then Beer's law approximates the CD signal as we change
the path length. We can go as small as 0.01-mm path length.
Samples are recoverable in 1-mm cells and larger.
NOTE: Non-UV absorbing buffers are required so that enough
signal transmits through the sample for CD detection.
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| Sample Submission Form |
Link to the Sample Submission
Form. This has more guidelines on sample preparation. |
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Training
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Conversions & Prediction Programs
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See the Biophysics Core Handbook for conversions
and other handy information used in CD studies.
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CD signal to Theta conversion.
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PENCE STABLECOIL,
by B. Tripet and R.S. Hodges, was designed to predict the location and stability
of alpha-helical coiled-coil conformations within protein sequences. The program
uses experimentally derived alpha-helical propensity and stability coefficients
as reported by Zhou et.al., 1994, Wagschal et.al., 1999 and Tripet et.al., 2000.
By summing the residue sresearchFacilities over a window width of 21, 28, 35 and
42, and comparing the total score to known globular and cytoskeletal coiled-coil
containing sequences, the program displays the region and probability (in kcal/mol)
that a particular sequence will adopt a coiled-coil conformation.
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Paircoil
(MIT), predicts the location of coiled-coil regions in amino acid sequences. To
analyze your own sequences with Paircoil, you can either use an online form or
download the program which provides a more powerful interface.
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K2D
M.A. Andrade, P. Chacón, J.J. Merelo, and F. Morán, European Molecular
Biology Laboratory, Heidelberg, Germany. K2D uses an algorithm for the estimation
of the percentages of protein secondary structure from UV circular dichroism spectra
using a Kohonen neural network with a 2-dimensional output layer. You can either
use k2d via a web server or get the program and run it on your machine.
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These investigators used a self-organising neural network to extract from a
set of circular dichroism spectra ranging from 200 nm to 241 nm the secondary
structure features present in the data.
This information is kept in a matrix result of hundred different trainings
of the neural network. k2d use this pre-calculated data to give you the result
upon your CD data. The run does not take more than a few seconds and provides
you with an estimation of the percentages of helix, sheet and random structure
of your protein.
k2d also gives the probable error in the estimation, based in the training
procedure results.
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ANTHEPROT
(ANalyse THE PROTeins) is the result of about 10 years of biocomputing activity
of a group
of the Institute of Biology and
Chemistry of Proteins. The main idea was to integrate into a single package
most of the methods designed for protein sequence analysis (1,2,3,4).
This simple idea was originally supported early in 1988!
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DICROPROT (DICHROism
of PROTeins) is the result of about 10 years of biocomputing activity of a
small group
of the Institute of Biology and
Chemistry of Proteins. The main idea was to integrate into a single package
most of the methods designed for the estimation of protein sequence secondary
structure derivation from circular dichroism experiments. The CD package was originally
a part of the ANTHEPROT
one (PC DOS version and IBM rs 6000). Some years ago, a new version for Windows
(3.11, Win95 or NT) has been developed (references)
and is now an individual program. The major goal in making DICROPROT is to help
the user to manage the spectra acquired with Jobin-Yvon apparatus.
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Sample Submission
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