Isn't the carboxyl group COO- and not COOH? Also, isn't the amino group H3N+ and not H2N?Sidechains are the part of amino acids that vary, depending on which amino acid you are talking about. Every amino acid has a similar structure, so the sidechain is what differentiates them. The diagram below shows the structure of every amino acid, with "R" representing the sidechain that varies.
This website shows the sidechains pretty well. In the diagrams on the left, all the sidechains are colored in red.
Typically, most sidechains are not modeled on your proteins, since not all sidechains will have a function. However, certain sidechains will be important to the function of the protein, so it would be important to model those sidechains. For example, in 2012, the pre-build was caspase-3. The active site for this protein has a cysteine and a histidine, so it was a good idea to model those particular sidechains in their correct locations on the pre-build.
Too often people get caught up in trying to put as much information on their build, and they lose sight of the fact that the build's main purpose is to show the FUNCTION of the protein. Since only a few sidechains actually contribute to the protein's function, these are the only sidechains you should worry about modeling.
They aren't available yet, but when they are, you will be able to find them at: http://cbm.msoe.edu/scienceOlympiad/participant4.phpWhere can we find out what proteins we're modeling for the on site builds?
You need to specify that you want chain A,When the fokI endonuclease protein is loaded on jmol, first we use the console to eliminate all amino acids besides 421-560. Then, we are left with two biomolecules. At first they appeared to be the same, however, when selecting one of them to view, jmol displays biomolecule 2 as have 53 more atoms than biomolecule 1. Does anyone know which biomolecule we are supposed to be modeling our protein after? Thank you!
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