Copyright Kevin McGregor

Beta-Sheet Proposer

What is Beta-Sheet Proposer?

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 Proposer 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. 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 41 solutions, i.e. PDB files (named 'sheet-000001.pdb'...). Use '-' instead of '+' to prevent output of PDB files. The third to last parameter is the maximum number of residues allowed in beta-sheets for comparison, here 999. The last parameter is the number of amino-acid classes for sequence analysis. Possible values are from 2 to 20. The classes are taken from the works of [6], Table II. The beta-sheet database has been compiled from the beta-sheet annotation of the program DSSP [4].

Tool: Extract STM Files

The Beta-Sheet Proposer program needs a special input file that can be generated from the database with the following program: This will generate the file 1DOK.1.stm that can be used as input for the Beta-Sheet Proposer program. Simply specify the 4-letter PDB code to extract from the database.

Tool: Viewing the Beta-Sheets Database

This program allows to view the beta-sheets contained in a .dat file. It launches RasMol on each NEW SHEET it finds in the database.

RESULTS

Figure 1: A beta-sheet topological graph from the monocyte chemoattractant protein 1 (MCP-1) (PDB code 1DOK).
PDB code 1DOK
Figure 2: Seventy-five 3-D models for the monocyte chemoattractant protein 1 (MCP-1) (PDB code 1DOK). All models are aligned on the first strand to show the conformational flexibility of this beta-sheet as found in the PDB. Colors are blue for strand S1, green for S2 and red for S3. Figures were produced using RasMol [1], Molscript [2] and Raster3D [3].
PDB code 1DOK
A) N-terminal side view.
PDB code 1DOK
B) C-terminal side view.
PDB code 1DOK
A) Face view.
PDB code 1DOK
B) bottom view.

REFERENCES

CONTACT

Marc Parisien
Created: 05/02/2004 Last update: 19/02/2004
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