Exercise 3: Protein Visualization Using Sybyl

The aim of this exercise is to analyze protein molecule using various SYBYL modules. To acess Sybyl the user needs an account in ABCC's SGI systems. Log into the host "nciiris.ncifcrf.gov". Before you start, initialize the environment by typing the following commands in a unix shell. The unix shell can be opened using the following commands, Left-Click on the Desktop menu to open the sub-menus and click on the Open Unix Shell. 

 
       setenv TA_ROOT /usr/local/fbscapp/sybyl
       setenv TA_BROWSER /usr/bin/X11/netscape
       source $TA_ROOT/lib/.login
After setting the ENV variables, type sybyl [See Fig.1] to invoke SYBYL.

Protein Modeling and Visualization:

Research Collaboratory for Structural Bioinformatics (RCSB) (formerly called Protein Data Bank (PDB)) is the single largest resource for biological macromolecular data. The web-link for RCSB is http://www.rcsb.org You can search the RCSB archive either with a RCSB code (ex Lysozyme, 7lyz) or with the protein name (Hen Egg White Lysozyme). The web-site has extra options (SearchLite,SearchFields,Status Search) to effectively search the structure archive.

Sybyl has a nice feature of connecting to the RCSB database and downloading the structure files directly to your computer. In this exercise we are going to download 7LYZ (RCSB entry) and analyze the structure using SYBYL.

  1. Biopolymer >>> PDB File >>> Get From FTP [See Fig.2]
  2. A radio window pops up asking for PDB/RCSB code (4-character PDB/RCSB code), enter the code 7lyz In the command prompt (window from where you typed sybyl ) enter your full email id. Please note that your email will not appear on the screen as you type [See Fig.3]
  3. A window pops [Fig.4] up asking "Do you wish read in pdb7lyz.ent?", answer yes by selecting Yes from the option menu and clicking on "OK" button.
  4. Answer the question for centering the molecule by clicking on Yes [Fig.5]. Now the protein is read in and the molecule will be centered on the sybyl's main screen. Also keep an eye on the command prompt window for the list of amino acid residues as Sybyl reads the PDB/RCSB file [Fig.6].
  5. Some useful mouse commands are the following: a) Zooming: Middle and Right buttons b) Right mouse to rotate c) Translation: Middle mouse button
  6. 7LYZ do not contain information about H atoms. Add Hs using the following command: Biopolymer >>> Add Hydrogens
  7. A sequence Expression window pops up, [see Fig.7].
  8. click on All to confirm that this operation have to be performed on all the atoms of the protein. At this point you will see the protein molecule in the Sybyl main window will be highlighted in green indicating the selection of all the atoms. The total number of monomers selected will also be given in the Monomer cell [see Fig.8].
  9. Hit OK to confirm your selection. Now the option box pop up. It has a question concerning which Hs to add ALL or Essential Only. ALL corresponds to both polar and non-polar hydrogen atoms. Essential_ONLY corresponds only to polar hydrogen atoms. Choose Essential_ONLY and hit OK .
  10. Polar hydrogen atoms will be added to the protein (shown in cyan color) and the total number of atoms added will be reported in the command prompt window. In this case it is 281 hydrogen atoms [see Fig.9].
  11. To look at the alpha C backbone do the following: Biopolymer >>> Display > C Alpha Only [see Fig.10].
  12. To label the amino acids in the alpha C backbone, go to View >> Label > Substructure to get the Substructure Expression box and click All to highlight all the alpha carbon atoms. Press OK to label them [see Fig.11].
  13. To unlabel, go to View >>> Unlable >>> Substructure and press All to select all the residues and hit OK.
  14. To display back all the atoms, do the following, Biopolymer >> Display >> Whole Molecule
  15. To display only selected atoms centered around an aminoacid (for ex TRP28) around a sphere of say 4 Angstroms, do the following: Go to View and select Undisplay Atoms Atom Expression Box opens up [see Fig.12]., change Atoms to Monomers and scroll down to residue # 28 (TRP28) and highlight it with your left-mouse. Click on Sets to open up the Sets.. radio box. Check the Sphere on and enter R=4 (ie. 4 Angstroms radius) and hit OK. [see Fig.13].. Now, you should see the residues which are located in 4 Angstrom radius are selected and are shown in green color [see Fig.14]. Now change Monomers to Atoms and click on invert to invert the selection. Note the number of atoms selected will be shown in the Atoms box. Finally, hit OK.
  16. To label the amino acid residues located in 4 Ang radius around TRP28, go to View >>> Label >>> Substructure which opens up the Substructure Expression menu, scroll down to highlight (with your left mouse) TRP28. Click on Sets and enter R= 4.0 and hit OK to choose all the residues displayed on your screen. Hit again OK to come out of the Substructure Expression radio box to see the aminoacid residues labelled.
  17. To display all the H-bonds, go to View >>> Display H-Bonds >>> Static to open the Atom Expression radio box. Change Atoms to Monomers and scroll down to highlight TRP28 residue and hit Sets and enter Sphere R = 4.0 and hit OK . Finally hit OK to come out of Atom Expression window. Option window pops up asking for the color of the H-bonds, choose YELLOW , and choose a filename for the display file (ex hbods.dsp) and hit OK [see Fig.15].
  18. To view the secondary structure, do the following:
  19. To print, use File >>> Print >>> Screen Capture Output/Plotter/Printer Output