SYBYL

Tutorial: Peptide building

The material presented in this tutorial is based primarily on the material given in the 'Tutorial Manual' of the SYBYL software package.

Preface

This tutorial illustrates the design of the biopolymer dictionary and some of the operations available for building, manipulating and editing biopolymers.
You will build a 14 residue segment of the H4 helix of thermolysin, using the PROTEIN biopolymer dictionary. This helix is involved in binding the Zn atom in the active site of thermolysin.

Fig.12 Active site of thermolysin,
showing Zn, HIS142, HIS146 and GLU166.
Helix H4 is colored green,
Other helices red, sheets blue, others yellow.

After this tutorial you will be able to:

Open a protein dictionary, and build a peptide sequence
Optimize the structure by relieving close contacts among the side chain atoms
Modify an existing peptide sequence

Before starting this tutorial, you should be familiar with the techniques introduced in the two previous tutorials ('Small molecule sketching' and 'Minimizing small molecules').

Clearing work areas

Clear all the molecule and display areas if necessary.
BUILD/EDIT >>> ZAP (DELETE) MOLECULE
If there is more than one molecule on the screen, click ALL, then OK to wipe them all.
RESET your screen if necessary.
Use the RESET gadget to reset EVERYTHING
Use the DISPLAY OPTIONS to reset to FULL screen mode.
Delete backgrounds, if any:
VIEW >>> DELETE ALL BACKGROUNDS

The BIOPOLYMER module

The BIOPOLYMER menu contains all the tools to build, edit, and analyze biopolymers.

The BUILD look-aside menu is used to construct biopolymers, including proteins, DNA, RNA, sugars and a combination of these.
The CONFORMATION and MODIFY look-aside menus are used to edit biopolymers that already have been built. One can excise, mutate, join residues, but also alter the conformation of a biopolymer.
The DISPLAY look-aside menu controls the display of molecules and as well as the display of ribbons and tubes (if your hardware supports this option).
The MONOMER DICTIONARY look-aside menu control operations relating to the biopolymer dictionaries.

Opening a biopolymer dictionary:
BIOPOLYMER >>> MONOMER DICTIONARY >>> OPEN...
Select PROTEIN from the dictionary list (press OK).
List the contents of the protein dictionary:
BIOPOLYMER >>> MONOMER DICTIONARY >>> LIST...
Select BRIEF for the listing mode (press OK).
A large amount of information is written to the text window. Pay particular attention to the conformational angle and state definition. They enable powerful operations in constructing, modifying and analysing biopolymers.

Building a peptide

Bring up the Build Biopolymermenu, as shown in fig. 13, and use it to define the sequence:
BIOPOLYMER >>> BUILD >>> PROTEIN...
Click on ILE ASP VAL VAL ALA HIS GLU LEU THR HIS ALA VAL THR ASP
Set the conformation option to ALPHA_HELIX.
Press BUILD.

Fig. 13 The Build Polymer menu.
Label the monomers:
VIEW >>> LABEL >>> SUBSTRUCTURE...
Press ALL in the Substructure Expression dialog box and press OK.
Each Calpha is labeled with the residue type and sequence number.
Renumber the sequence: BIOPOLYMER >>> MODIFY >>> RENUMBER SEQUENCE...
Select ALL from the Sequence Expression dialog box and press OK.
Enter 137 in the next dialog box and press OK.
Name the molecule:
BUILD >>> MODIFY >>> Molecule...
Select NAME (press OK).
Select M1:<no name> (press OK).
Type HELIX4 for the molecule name and press OK.
Color atoms according to atom type:
VIEW >>> COLOR >>> BY ATOM TYPE
Add H atoms:
BIOPOLYMER >>> ADD HYDROGENS...
Select ALL, press OK,
Select ALL and press OK again to add all instead of the essential_only H atoms.
Save the current model:
FILE >>> SAVE AS...
Type helix4.mol2 in the file selector box, and press SAVE.

Modifying the conformations of the HIS142 and HIS146 sidechains

By rotating and scaling the molecule you will notice that both histidine monomers are located at the same side of the helix. The sidechains are oriented very similarly, but since these histidines stablize a Zn atom in the active side of thermolysin, their relative orientation should be modifyied to resemblem the orientation as illustrated in fig. 12 and schematically depicted in fig. 14.

Fig. 14 Relative orientation of His142 and His146
to enable the stabilization of a Zn
in the active site of thermolysin.

Preparing for manual torsion variations:
Undisplay part of the molecule to facilitate atom selection by
VIEW >>> UNDISPLAY ATOMS...
Change the Atoms: box into Monomers: and pick any atom in residues 137 ... 141 and 147 ... 150
Then, change the Monomers: box back to Atoms:, activate ATOM TYPES... and toggle the H box on. Click on OK in both the atom type select box as well as in the general atom selector menu (only residues 142 through 146 should be visible).
VIEW >>> LABEL >>> ATOM ID...
Change the Atoms: box into Monomers: and pick any atom in residue His142 and His146.
Monitor distance of the 'Nepsilon' atoms of the histidine rings:
VIEW >>> MONITOR >>> DISTANCE...
Select ADD and press OK.
Select atoms N47 and N81 and press END.
The distance between these atoms (6.87 Angstrom) will be displayed in yellow.
Rotating around bonds:
Activate the Rotatable Bonds gadget which initially looks like fig. 15 (left side).
Click on the empty box just below the 'Q' in the Rotatable Bonds menu and then pick atoms 33 and 40. The value of a torsion around this bond will be given on the right side of the 'dials' in the same menu.
Click on the next empty box (below the '1') and click on atoms 40 and 43.
Continue defining rotatable bonds using atoms 65 and 74, and then using atoms 74 and 77, so that the Rotatable Bonds menu looks like the one in fig. 15 (right side).

Fig. 15 Left side: Initial Rotatable bonds menu,
Right side: After specifying the four bonds in the histidine side chains.
Click on the 'dials' in Rotatable Bonds menu and watch the molecule changing, while the monitored distance between the histidine 'Nepsilon' atoms previously defined is updated also.
Try to rotate the four bonds in such, so that the monitored distance is close to 3.13 Angstroms and the angle between the rings is approximately 105 degrees (which cannot be monitored). (The values of the torsions in the Rotatable Bonds menu should be close to 84, 275, 271 and 135 respectively.)
Freeze the current orientation and save the structure:
In order to make the rotations permanently, the screen coordinates have to be transfered to the memory coordinates.
VIEW >>> FREEZE VIEW >>> BOTH...
Select ALL and press OK.
Use the FILE >>> SAVE AS... to write this model to a file.
use helix4A.mol2 as file name and press SAVE

Compare the new model with a crystallographically determined thermolysine HELIX4

Read experimental data on HELIX4:
Type in the text window (or use the equivalent from the menus)
mol2 in m2 ta_demo:thermolysin4A.mol2 and press Enter
Display the non-H part of your own model of HELIX4 and label the structures:
Type in the text window (or use the equivalent from the menus)
display m1(*-<h>) and press Enter,
label subst m1(*) and press Enter,
label subst m2(*) and press Enter.
Superimpose the Calpha atoms:
Use ANALYZE >>> FIT ATOMS... to bring up the dialog box.
Select Add... and pick all Calpha atoms pairwise, starting with either model.
Select END when done, and SOLVE the least squares problem.
Click on DONE and RESET >>> EVERYTHING as in the previous examples.

This concludes the 'basic' peptide building tutorial.