Select the sequence to highlight it in the 3D viewing window. For the hemoglobin-myoglobin alignment examine the insertion in the myoglobin sequence. Do the sequence aligned portions appear to align in space? Use Cn3D to visualize both a spatial alignment AND to project the sequence alignment onto the 3D structures. Compare this structure to human myoglobin (1A6M) and Drosophila melanogaster globin (2BK9). A simple example is PDB ID VS48, the human hemoglobin. Now we'll use Cn3D4.1 to view structural alignments of two proteins with related 3D structures and related sequences. How many strands does it contain by your count? How does this B-sheet get described in the PDB file? Examine the largest B-sheet in this protein. Is the B-sheet with the most strands in the protein predominantly parallel or anti-parallel? How many helices does this molecule contain by your count? According to the annotation in the.
Try to trace the chain from N-terminus to C-terminus. Excluding glycine, proline, and pre-proline, which aa(s) is/are in the disallowed region? View the Ramachandran plot for this protein (PDB left hand side link to Geometry -> MolProbity Ramachandran Plot). What atoms or molecules other than standard amino acids in the polypeptide chain does this structure contain? pdb structure file (the link near the structure ID). How many protein chains make up this structure? Propose two alternate ways that one could go from having the "clamp" and the "DNA thread" separate to having the clamp around the middle of the thread. Assume that somehow, you have to get this "clamp" around the very middle of a very long DNA molecule.
I would like you to think in a very physical way about biological problems. Is this "hole" approximately large enough for a DNA molecule? (Structure 1DH3 linked above shows DNA.) Give a brief answer. Give the distance between the atoms that you measured.
Measure the approximate distance across the "hole". Give figures for the longest dimension (across the hole) and thickness (edge on so the hole is not visible). Measure the approximate size of this multi-protein complex. Color the molecule by secondary structure, make the water visible, rotate so the "hole" is obvious, and take a "picture" PASTE HERE. Notice that first you need to select a portion of the structure, then pick a command to change the display of the selected item. Explore the viewing options, color options, etc. Clicking on the view pane while holding down the 'Cntrl' key brings up command menus. View the structure of 1AXC from the PDB database JMol viewer. To change the color of secondary structure type "select helix " or "select sheet " and then use the menu option to set the color. To select a single protein chain, open the Console, then to select chain 'D' type (without the quotes), "select *:D ", and hit the execute button. Instructions on using JMol is on the list of links above. To start the lab I'll demonstrate the use of the JMol structure viewer.
#Look at specific amino acids jmol how to
Learn how to view and manipulate protein structures using Cn3D and the Chime-based Protein Explorer. Understand PDB entry and structure analysis tools. Learn how to search and use the PDB and Entrez structure databases.