Copyright Kevin McGregor

Beta-Alpha-Beta Builder

What is Beta-Alpha-Beta Builder?

Beta-Sheet Proposer
The Beta-Alpha-Beta Builder is a program that adds alpha-helices onto a beta-sheet. Both loops of each helices have the constraint of beeing connected somewhere on the beta-sheet. The program first backtracks on loop and helix fragments from the Protein Data Bank to build each beta-alpha-beta units individually, then backtracks on these units to find non-clashing helix pairs.

PROGRAM

The featured beta-sheet is from Baker's Top7 de novo protein (PDB code 1QYS). The result of the execution should give you 53 solutions, i.e. PDB files (named '1qys-00001.pdb'...). The loop and helix databases has been compiled from the annotations of the program DSSP [4] on the culled PDB [7]. The program's parameter needs further explanations:

RESULTS
The following 3D structures have been generated with this command:

./bab.exe ./baker.helix.bab ./1qys.sheet.pdb ./loops.25.dat ./helices.25.dat 1.0 5.0 1.0 1.5

Figure 1: Fifty-three 3-D models for the two beta-alpha-beta units in Baker's Top7 protein (PDB code 1QYS). All models are aligned on the beta-sheet to show the conformational sampling. The models are at least 1.5 Angstroms from each other. Colors are from blue for N-terminus to red for C-terminus. Notice that all beta-alpha-beta units are all "on top" of the beta-sheet, in accord with the right-handedness of connections in proteins. Figures were produced using RasMol [1].
top view
A) Top view.
bottom view
B) Bottom view.
front view
A) Front view.
back view
B) Back view.
side view 1
A) Side view #1.
side view 2
B) Side view #2.

optHelix
Since the positioning of the alpha-helices on the beta-sheet is a purely geometrical procedure we are left with 3D structures in which the hydrophobic moments of the alpha-helices may not be optimized. We have made a program that optimizes the HFS score [9][10], therefore the hydrophobic moments, by rotating the alpha-helices on their main axis to the best of the HFS score. The program takes for input a PDB file and will optimize any helices that are described in the proper HELIX PDB records. The original file is backed-up (with a .bak suffix) then replaced by the optimized helices.

The result of the execution on the first model in the PDB file 1POU:
Loading PDB file: `1pou.pdb'
Initial energy: -3.70295
Final energy: -4.10463
Helix 1 has rotated  +29 degrees
Helix 2 has rotated   -2 degrees
Helix 3 has rotated  -23 degrees
Helix 4 has rotated   -8 degrees

addFrag
Need to add some beta-turns or some loops into your 3D models? use addFrag! It will select the best fragment from the PDB to bridge the gap between any pair of residues. It does not optimize the loop closure afterwards, though, but the selected turn/loop could be a good starting configuration for a subsequent minimization.

WARNING: The PDB file will be replaced with a version that includes the turns/loops; make a copy of it before launching addFrag. To add turns, use -T; to add loops use -L instead. To zap the PDB file when a fragment cannot be inserted satisfactorily use -Z 1.5, as in:
./addFrag.exe -T -Z 1.5 baker.all.bab 1qys.sheet.noturn.pdb loops.25.dat
Lower values to Z will produce better chain closure but the probability to satisfy it will drop accordingly.

REFERENCES

CONTACT

Marc Parisien
Created: 19/10/2004 Last update: 19/10/2004
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