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You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
The Initial Search
We were given a Protein with a predicted structure from Uniport and an unknown function. We are trying to find the function of the protein. We did this by first using computational tools like Blast, Dali, and Interpro to help us find potential substrates.
The first computational tool we used was Blast the results of which are shown below on Table 1.
<img src="blob:chrome-untrusted://media-app/376d84bf-5fc2-4328-a234-9d0eb5134dde" alt="Screenshot 2023-04-22 11.49.44 AM.png"/>
Molecular Docking
From the initial search throughout all of the computational tools, we decided that our putative kinase was potentially a glucokinase. We docked other sugars along with glucose in figure 1. taking in consideration of the DNA binding domain found in the InterPro results we docked DNA nitrogenous bases and nucleosides which are show in Table 5.
[figure 1 sugars docked.
[table 4 results docked sugars]
[docked nucleoside structures figure 2]
[table 5 results docked nucleosides-bases]
From the results of the docked sugars, nitrogenous bases, and nucleosides, we determined that guanosine was a strong potential substrate but still wanted to test glucose due to the computational tools results since glucokinase was a common output in all of our searches.
We used Pymol to visualize the intermolecular interactions in the active site with guanosine (figure 3) and glucose (figure 4).
Structural Highlights
with 397 amino acids. It's secondary structure is made up of alpha helices, beta sheets, and random coil. Through docking we were able to identify possible amino acids involved in the active site of P76586.
Results
Our protein of interest has a weight of ≈44.53kD. When analyzing SDS PAGE (figure 5) we were slightly concerned we weren't working with our protein of interest. We didn't get a great image out of SDS, if there were more time we would run again with more protein in the well so that we could see it better. We also made the mistake of not running our pre and post inductions samples.
Conclusions
This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
