OUR STEP-BY-STEP PROCESS
1. Use the to download a protein in the PDB format (to be opened in Wincoot) that has one or more disulfide bridge in it. To do so, use the advanced search tool and choosing the query type "Number of Disulfide Bridges." Set the maximum and minimum number of disulfide bridges and search.
2. Click "draw" in the upper right corner of the Wincoot file. Click on chain A and a list of amino acids will drop down. Scroll through the amino acids to find one labelled "CYS" (cysteine). Click on this amino acid and it will take you to the disulfide bridge in the protein.
3. Click "measures" in the upper right corner of the Wincoot file. Then, select "distances and angles." Depending on what you are trying to measure, choose the option that is necessary for the data you're collecting. (We used the "torsion," "angle," and "distance" options, for reference.)
4. The data will appear on the top center of the Wincoot window.
To measure bond lengths in cysteine:
a. Select "distance" from the "measure" option.
b. To measure the X1 bond length, select the beta carbon and the alpha carbon.
c. To measure the X2 bond length, select the alpha carbon and the sulfur closest to it.
d. To measure the X3 bond length, select both of the sulfurs.
To measure torsion in cysteine:
a. Select "torsion" from the "measure" option.
b. To measure the X1 torsion, select the nitrogen, beta carbon, alpha carbon, and sulfur, in that order.
c. To measure the X2 torsion, select the beta carbon, alpha carbon, and the two sulfurs, in that order.
d. To measure the X3 torsion, select the alpha carbon, two sulfurs, and the alpha carbon on the other side of the sulfurs, in that order.
To measure angle in cysteine:
a. Select "angle" from the "measure" option.
b. To measure the X1 angle, select the beta carbon, alpha carbon, and sulfur.
c. To measure the X2 angle, select the alpha carbon and the two sulfurs.
d. To measure the X3 angle, select the two sulfurs and the following alpha carbon.
Dr. Offermann and Dr. Myers at Davidson College introduced us to WinCoot, a program that allows us to visualize the proteins and measure dihedral angles by hand.
How to Measure Angles with Wincoot
Kaelan van Cleef walks through the process of measuring Bond Lengths, Bond Angles, and Torsional Angles in WinCoot using Leucines in Insulin as an example.
PyMOL Step by step tutorial Using Phenylalanine
1. To get a PDB file uploaded to the program, go to file --> Get PDB… and then enter in the 4 letter PDB code in the PDB ID option.
2. To display the residue sequence of the protein, go to display --> sequence
3. Next, in the displayed sequence, highlight the chain of the protein that contains the residue(s) that you want to measure
4. Then, hide everything and show only the selected chain of the protein as licorice sticks
5. Next, make sure the mouse selection mode is atoms. Press Mouse --> selection mode --> atoms
6. Next, select your desired residue from the displayed sequence. Make sure that it is in the chain that you have selected!
7. Now orient your selected residue to make measuring easier.
8. Now it is time to measure. Press wizard -> measurement and select what kinds of measurements that you want. Make sure that you press the atoms in the correct order for the measurements.
To change the kind of measurement, just choose from this tab. Make sure that you select the atoms in the correct order.
For bond lengths, select two consecutive atoms
For bond angles, select three consecutive atoms
For torsional angles/dihedrals, select four consecutive atoms