Molecular viewers Preston University Islam abad 1
1
Molecular viewers Preston University Islam abad
Protein visualizationsAmino acid SequencesTranslated SequencesSignature Sequences----Motifs
and PatternsConserved Sequences among
Orthologues and Paralogues
PROSITE---a pattern identifier
A short guide to Molecular Visualization using some of the tools in the Jmol program
http://jmol.sourceforge.net/
The Jmol applet opens automatically from the Protein Data Bank
www.pdb.org brings you to the U.S. portal for the world-wide PDB
The Protein Data Bank is an international consortium
Structures submitted to the Protein Data Bank have a 4-character accession number
3COQ
Let’s look for Gal4p, which has the PDB accession number 3COQ(You can find PDB numbers on the Protein tab at SGD)
Begin your project by obtaining the PDB file for your protein
Summary page for PDB records includes the literature reference and MANY links
Click here to begin using Jmol
Drag the structure with your mouse
Default Jmol view
Uses the Cartoon scheme
With Structure colors
Structure colorsα-helices are pinkCoils are whiteβ-sheets are gold (none shown)DNA is purple
Click on Jmol_S to access commands that will customize your structure
Begin by using the Select command
Jmol can work on the whole structure of parts of the structure at one time
In the next few slides we’ll work on only the protein structure
Select “Protein”Next, select “All”
Allows you to work on the whole structure, or just the protein (or nucleic acid or cofactors)
First, we’ll choose a scheme to display the protein.
Begin by choosing STYLE at the main menu.
Let’s look at the structure with these different rendering schemes
Spacefill Ball and stick Sticks
Wireframe Cartoon Trace
Cartoon and trace are shown in structure colors
Gal4p is shown in several schemes in either CPK or structure colors
CPK (Corey-Pauling-Koltun ) is a color scheme for atoms (C=grey; O=red; N=blue; S=yellow)
Add some color – choose color from the main menu
Atoms can be colored with a color of your choice or with a coloring scheme
Group color schemeN-terminal is blue (cold)
C-terminal is red
Amino acid scheme
Gives a different color to each amino acid
Chain color schemeEach polypeptide gets a
different color (Gal4p is a dimer)
Finishing the image
Select the nucleic acid – choose the ball and stick rendering scheme (default colors are CPK)
Small molecules in the structures are considered “Hetero” atoms
After selecting hetero, we’ll use the spacefilling scheme for the Zn atoms in the Zn-fingers and color them orange
In addition to Zn atoms, a molecule of 2-methyl-2,4-pentanediol is bound to the structure
Once you’re finished your structure, it can be exported in a variety of file formats
Thanks