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Contrast Calculator

Calculates the neutron and x-ray scattering length density (SLD), contrast and I(0) values for a single molecule or complex consisting of proteins and/or nucleic acids, as well as other compounds such as polymers, lipids and carbohydrates, based only on sequence or chemical formula information.

Link to PDF file of a step-by-step tutorial using SASSIE-GUI (stand-alone)

Contrast_Calculator

Link to a ZIP file containing example files required to complete tutorial

Files

Accessibility

The Contrast Calculator module is accessible from the Tools section of the main menu.

Basic Usage

The purpose of the module is to calculate neutron and x-ray SLD, contrast and I(0) values from biomolecular complexes to assist in experiment planning. The module handles complexes consising not only of proteins and nucleic acids but also polymers, lipids, surfactants, carbohydrates, etc. Single species not in complexes can also be handled.

Notes

Case 1: Protein/DNA Complex in water with 0.15 M NaCl

This is an example of a protein-DNA complex consisting of two synapsis-deficient Cre(A36V) recombinase molecules bound to a single loxP site. Two FASTA files are available; one contains the sequence of a single Cre(A36V) protein and the other contains the sequence of the loxP DNA.

Screen Shots and Description of Input Fields

The top of the Contrast Calculator screen contains the main user input.

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The Optional Input is located below the main user input

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Example Output

The output screen lists the match points for the protein and DNA components in the complex as well as for the entire complex. The output also shows plots of the calculated neutron SLDs, contrasts, I(0) and sqrt[I(0)] as a function of % D2O in the solvent since the complex doesn't contain more than 2 components. Note that roll-over help will indicate options to resize, zoom and reset the view of the plots. Resultant files containing the SLD, contrast and I(0) values are written to a new directory, "contrastcalculator", within the run0 directory.

From the SLD and contrast plots as well as the match point values, it is clear that the protein match point is very close to that of the entire complex. Therefore, it will not be possible to make a measurement at the protein match point in order to observe the scattering from the DNA component, as this will be too close to the match point for the entire complex and there will be no measurable signal. A measurement can be made at the DNA match point of 62% D2O in order to observe the scattering from the protein component. However, the I(0) value at 62% D2O is very low at 1 mg/ml and a higher concentration would be needed to obtain a reasonable signal.

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./run_0/contrast_calculator/crelox_izero.txt
./run_0/contrast_calculator/crelox_sld.txt
./run_0/contrast_calculator/crelox_contrast.txt

Files Used and Created

Case 2: Protein/Deuterated Protein Complex in water with no additional components

This is an example of a protein-deuterated protein complex consisting of a skp chaperone trimer and a 50% deuterated unfolded outer membrane protein, ompA. Two PDB files are available; one contains the structure of the skp trimer and the other contains the structure of the ompA membrane protein.

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Screen Shots and Description of Input Fields

The top of the Contrast Calculator screen contains the main user input.

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The Optional Input is located below the main user input

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Example Output

The output screen lists the match points for the protein and 50% deuterated protein components in the complex as well as for the entire complex. The output also shows plots of the calculated neutron SLDs, contrasts, I(0) and sqrt[I(0)] as a function of % D2O in the solvent since the complex doesn't contain more than 2 components. Note that roll-over help will indicate options to resize, zoom and reset the view of the plots. Resultant files containing the SLD, contrast and I(0) values are written to a new directory, "contrastcalculator", within the run1 directory.

From the SLD and contrast plots as well as the match point values, it is clear that both the protein and deuterated protein match point are well separated from that of the entire complex. Therefore, it is possible to make measurements at both contrast points, provided that the I(0) values are sufficient to obtain a measurable signal at those match points. In this case, concentrations higher than 1 mg/ml would be needed to obtain a reasonable signal at these match points.

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./run_1/contrast_calculator/skpompa_izero.txt
./run_1/contrast_calculator/skpompa_sld.txt
./run_1/contrast_calculator/skpompa_contrast.txt

Files Used and Created

Case 3: Protein/lipid Complex (Nanodisc) in water with no additional components

This is an example of a protein/lipid nanodisc consisting of 2 MSP1D1 proteins and 130 POPC lipid molcules. A FASTA file containing the sequence of MSP1D1 is available. The chemical formula for POPC, C42H82NO8P, will be used for the lipid component of the complex.

Screen Shots and Description of Input Fields

The top of the Contrast Calculator screen contains the main user input.

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The Optional Input is located below the main user input

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Example Output

The output screen lists the match points for POPC (Molecule 1) and protein components in the complex as well as for the entire complex. The output also shows plots of the calculated neutron SLDs, contrasts, I(0) and sqrt[I(0)] as a function of % D2O in the solvent since the complex doesn't contain more than 2 components. Note that roll-over help will indicate options to resize, zoom and reset the view of the plots. Resultant files containing the SLD, contrast and I(0) values are written to a new directory, "contrastcalculator", within the run2 directory.

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./run_2/contrast_calculator/nanodisc_izero.txt
./run_2/contrast_calculator/nanodisc_sld.txt
./run_2/contrast_calculator/nanodisc_contrast.txt

Files Used and Created

Visualization

None

Reference(s) and Citations

Small-angle scattering contrast calculator for protein and nucleic acid complexes in solution K.L. Sarachan, J. E. Curtis, S. Krueger, J. Appl. Cryst. 46 1889-1893 (2013). BIBTeX Citation, EndNote Citation, Plain Text Citation

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