Copyright Kevin McGregor

Beta-Sheet Builder

What is Beta-Sheet Builder?

Beta-Sheet Proposer
The mathematical graph theory has been applied to protein beta-sheets. These beta-sheets can be encoded in graphs, where vertices are the residues of the beta-sheet and the edges are the various topological relations between the residues. The topological relations can be one of 1) covalent peptidic bond between adjacent residues. 2) H-bond between residues of distinct strands. 3) Beta-sheet partnership; residues that are side-by-side in the beta-sheet. These topological features happen to be calculated by the program DSSP [4]. The topological graphs, along with their associated 3-D atomic coordinates, of proteins found in PDB [5] have been compiled in a database. Given a beta-sheet topological graph, the Beta-Sheet Builder program will seek the database for subgraph isomorphism and output the 3-D coordinates of the graphs that matches the given input graph. That way it is possible to go from a 2-D beta-sheet description to a 3-D atomic model. The difference between the Beta-Sheet Builder and the Beta-Sheet Proposer is that the Builder is less limited on the generation of topologies since the input sheet graph is split into pairs of strands. The Builder is thus able to build beta-sheet unobserved yet in PDB, as long as each pair of strands can be found in the PDB. A perfect example is Baker's Top7 beta-sheet [6]; although the complete beta-sheet has not been in PDB Select, the Builder is able to generate 3D coordinates for that sheet since each strand pairs are fairly numerous in PDB. See article for more details.

PROGRAM

The featured beta-sheet is from the monocyte chemoattractant protein 1 (MCP-1) (PDB code 1DOK). The result of the execution should give you 26 solutions, i.e. PDB files (named '1DOK-000001.pdb'...). The beta-sheet database has been compiled from the beta-sheet annotation of the program DSSP [4]. The program's parameter needs further explanations:

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

./psb.exe ./baker.stm ./pairs.25.bspider.dat 0.5 0.5 0.4 9999 1.0

Figure 1:579 beta-sheet 3D models for Baker's Top7 beta-sheet (PDB code 1QYS) [6]. Each beta-sheet is at least 1.0A apart from all the other beta-sheets. The sheets are aligned on the [13-19] strand, which is a border strand. The figure was produced with RasMol [1].
PDB code 1QYS
A) Side 1 view.
PDB code 1QYS
B) Side 2 view.
PDB code 1QYS
C) N-terminal side view.
PDB code 1QYS
D) C-terminal side view.
Figure 2: Accuracy test of the Beta-Sheet Builder on the beta-sheet of 1TML. The crystal structure has light grey cylinders while best RMSD (0.83A) structure has dark grey ones. Strand ribbons are pictured for the crystal structure. The image was produced using RasMol [1], Molscript [2] and Raster3D [3].
PDB code 1TML
Figure 3: Flexibility test of the Beta-Sheet Builder on the beta-sheet of 1TML. The crystal structure is in red while the worst RMSD rebuilt structure is in blue. Both structures are aligned along the strand 40 to 42. The high RMSD (7.88A) comes from the fact that the rebuilt structure chooses a different path as soon as the third strand from the top. The image was produced using RasMol [1], Molscript [2] and Raster3D [3].
PDB code 1TML

REFERENCES

CONTACT

Marc Parisien
Created: 23/09/2004 Last update: 23/09/2004
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