3/18/2024 0 Comments Jmol color scheme![]() To select and display a specific sidechain, you will use the select command followed by the amino acid residue number and end with and sidechain. All of the other atoms within the amino acid are not displayed, including the Sidechain, also called the R-Group.īut sometimes you may wish to display a specific amino acid residue's sidechain because it is important to telling the story of your protein, such as a sidechain that binds to a substrate or holds the protein together, even if the rest of your protein structure remains represented in backbone format. In backbone format, only the position of the alpha carbon in each amino acid is shown, representing a bend or kink in the backbone. Most protein models designed with the CBM's Jmol User Design Environment for 3D Printing use Backbone Format. Because of this, the specific amino acids in a protein are very important and directly relate to the protein's structure (shape) and function (job). You now know enough about how proteins are depicted to explore the four levels of protein structure.Proteins are long linear sequences of linked amino acids that fold up into complex 3-dimensional shapes based on the order of their amino acids. User Defined Color Scheme: Purple and Green Here are some other examples of user defined color schemes. You'll learn more about these proteins later in the tutorial. They colored the two protein backbones differently, then added important sidechains in CPK coloring. This model was designed by the 2011 Mount Mary CREST Team. User Defined Color Scheme This is an image of GATA-1 and FOG-1, proteins important in regulating which genes are turned on in development. Here alpha helices are colored red and beta pleated sheets are colored yellow.ĬPK Coloring This standardized coloring scheme uses a specific color for each type of atom. Zinc finger motifs are often found in proteins that bind to DNA (shown here in pale blue). Here the chains are colored differently to visualize how they interact.Ĭolor Structure This view displays secondary structure of a zinc finger protein (1ZAA.pdb). It is sometimes called the alpha carbon backbone.īall and Stick This view shows each of the atoms as balls, with sticks to indicate the bonding between atoms.Ĭombination Display Each representation has advantages and disadvantages.Ĭolor can be used effectively to communicate information about protein structure.Ĭolor Chains Some proteins, such as insulin (2HIU.pdb), consist of more than one peptide chain. Spacefill Spacefill depicts all atoms at their relative diameter.īackbone This display only shows the central carbon atom (the alpha carbon) of each amino acid, with a solid line connected adjacent amino acids. Shown below is insulin (2HIU.pdb), a hormone that regulates blood sugar levels. There are three common formats for displaying proteins each is used to show different features of the protein. #1888 identifies the atom number in the pdb file. is the 3 letter amino acid abbreviation (or 1 letter nucleotide, if it is a nucleic acid)ī identifies the chain name in the pdb fileĬA identifies the atom type. If you hover over an atom in Jmol, a popup window will identify the atom in the format: A Jmol Quick Reference Sheet and Jmol Training Guide are available if you want to play with the images. ![]() ![]() You may spin the protein (left mouse button click and drag), or, if you wish, you may use Jmol commands to explore the protein further. Once a protein appears in the Jmol window, wait until the image stops moving before pushing a button to execute another script. Throughout the tutorial, clicking on the buttons will launch a Jmol (Jsmol) image of the protein on the screen at the right. The PDB accession numbers are provided for each protein in this tutorial, in case you want to explore the proteins further. These structures are deposited in the Protein Data Bank (PDB) for use by researchers, educators and students. All the proteins used in this tutorial have had their structures determined using X-ray crystallography or NMR. This section is an introduction to a variety of ways of depicting proteins, as well as some common color schemes used in depicting proteins. This tutorial focuses on protein structure and the intramolecular forces that are involved in protein folding and stability. ![]()
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