User:Eric Martz/Sandbox 11

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Proposed title: Knots in Proteins: Methods

This page describes technical details of the methods used for the morph at Knots in proteins.

The PDB file that displays the animated morph of the protein knot being "shrunk" is Image:1yve i knot morph.pdb. This file contains 51 models. Model 1 is a slightly smoothed backbone trace of the knotted segment of chain I in 1yve, namely 234 residues, sequence numbers 312-545. Model 51 is a simplified knot, which is the result of shrinking the backbone while keeping the ends fixed in space. These models were kindly provided by William R. Taylor (Division of Mathematical Biology, National Institute for Medical Research, the Ridgeway, Mill Hill, London UK). These models represent the residues with alpha carbon atoms only, and all residues are labeled GLY.

For the website developed in 2000, the coordinates of these models were reduced (using the MS-DOS PDB Tools program shrink.exe) so the visualization plug-in MDL Chime would automatically connect the alpha carbon atoms (some being unrealistically distant from each other) with a backbone trace. However, Jmol did not connect consecutive alpha carbon atoms due to the mixture of unrealistically small and large distances between them. Therefore, the following script was employed to generate bonds (wireframe) in Jmol between consecutive alpha carbon atoms:

select all # all 51 models
wireframe off
backbone off
spacefill off
connect delete # deletes all the automatically generated inter-atomic bonds
# now connect consecutive alpha carbons. model 1 contains 234 alpha carbons. model 51 contains 14.
for (i=1; i<=234; i++)
	ii = i + 1;
	connect (atomno=i) (atomno=ii);
wireframe 0.05 # display the new connections
color group

The morph for the comparison example that has no knot, 1tph chain "1", is in Image:1tph 1 noknot morph.pdb. Similar methods were employed, adjusting the maximum residue count in the above script from 234 to 242.

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Eric Martz

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