SMART Project Protein Structure and Folding: The WSSP has teamed up with the Center for BioMolecular Modeling to provide students with the opportunity of creating a physical model of a homolog of one of the proteins that was identified in the screen of the cDNA library. Only one model can be made for each high school. The models above were created from left to right by students from Colonia, West Windsor-Plainsboro South, East Brunswick, and Pingry High Schools for the 2008-2009 WSSP Poster Forum.

High Schools wishing to create a physical model of their protein need to provide the following information by e-mail to Andrew Vershon or Sue Coletta:

To get started:

1. Students who have identified a clone from the cDNA library that codes for a full or partial protein should first search if a structure of a homologous protein has been determined by x-ray crystallography of NMR. This can be done by performing a NCBI BLASTP search with the predicted protein sequence from their clone and then examining if any of the matches that were identified in the Conserved Domain Database (CDD) contain structures (see lecture notes on CDD). Alternatively the students can search the Protein Data Bank (PDB) for the structure.

2. Perform a BLAST2 sequences alignment between the predicted protein sequence from the Artemia clone and the protein sequence of the protein you will be modeling. This alignment is helpful to identify conserved residues on the structure model.

3. Download the pdb file (e.g. 1A3N.pdb) with the coordinates of the protein structure and use a version of the RasMol program that has been designed to create the physical models using Rapid Prototyping technology.

4. Students should use the commands in RasMol to create a script file that will display the protein using the format features (spacefill, backbone, etc) and the colors they prefer. A color scheme may be used that indicates identical or similar residues as predicted by the sequence alignments; the active site of the protein; structural components such as alpha helices and beta-strands; etc. If the protein sequence from the database is strongly conserved with your protein, you may want to highlight the differences.

Note: Cartoons and strands don't build well.  Wireframe and ball and stick work well (see sizes below).  Spacefill doesn't really show the protein structure well, just the overall shape.  It depends on what you are trying to show.  A typical structure may show a backbone model with few selected sidechains in ball and stick.  

Standard sizes that build well:
backbone 300
wireframe 225
spacefill 275
hbonds 225

The commands wireframe and spacefill combined give a ball and stick.

Also, it is important when doing sidechains to use the command:
select *** and (sidechain or alpha)
where *** is the amino acid number
Otherwise you get a bumpy backbone.

There's a new tutorial at: http://cbm.msoe.edu/includes/jmol/rasmol.php (only available in IE).  It covers all the important information for building a model.

RasMol Training Guide - Below are resources to help with creating a model using RasMol. The RasMol Training Guide was developed by Shannon Colton at the Center for BioMolecular Modeling. Additional information can be found on the CBM RasMol Resource Page