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Recipe: Missing Ligand 1.0.1 -- brow42
Created by brow42 79 415
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Name: Missing Ligand 1.0.1 -- brow42
ID: 46378
Created on: Thu, 06/27/2013 - 21:14
Updated on: Fri, 11/29/2013 - 01:42
Description:

Add bands for missing constraints. Pick the bond shape for the missing atom and band a group of atoms in that shape. Distances set by atom type. Yes, I know it has trouble guessing the right group.



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brow42's picture
User offline. Last seen 3 days 9 hours ago. Offline
Joined: 09/19/2011
Groups: None
Missing Ligand 1.0

Sometimes the atoms of a protein bond to a metal ligand. Unlike the puzzles with large organic ligands, these small metal clusters are usually left out of the puzzle.

These metal atoms usually bond to the sulfur in cysteines in simple geometric patterns. This recipe lets you pick a shape, and lets you band the sulfurs into the shape they would have if they were bonded to the metal.

Common in puzzles with names like porphyrin, ferredoxin, ruberedoxin.

* Missing Ligand
*
* Residues should be bonding to a ligand, which is missing
* The ligand could be replaced by constraints
* If constraints are missing, then make bands
*
* Version 0.1 June 28 2013 brow42

* Version 1.0 Nov 28 2013 brow42
* Added tetrahedral symmetry
* Will now work witih O-terminal cysteine
* Added Help

Joined: 09/24/2012
Groups: Go Science
How to use?

It identified ferredoxin on puzzel 814, but I don't see it on screen and I don't know what to do next. Which kind of view should we use?

brow42's picture
User offline. Last seen 3 days 9 hours ago. Offline
Joined: 09/19/2011
Groups: None
How to use

The script cannot really guess what to do, so it relies on the user a lot.

Suppose the puzzle description says ferridoxin, and you have 5 cysteines. One type of ferridoxin bonds two iron and 4 cysteines together. You would check the 'M2S2Cys4' box.

The script knows what the positions of the atoms should be for this bonding (a flat rectangle). So it will bond the sulfurs of 4 cysteines with strong bands, with the lengths of the sides and diagonals of the rectangle.

Which 4 cysteines? The 4 that are most "grouped up". So, pick the 4 cysteines you think should be bonded to the iron and pull them together. Make two groups of two; the close pairs will be the short side of the rectangle. Make the fifth cysteine be far away. Now you can run the script and it will band the sulfurs.

If you don't know what kind of bond the protein has, you can experiment based on shape, like 4 cysteines bonded to one atom in a tetrahedron.

The script isn't smart enough to handle more than one ligand site. It has enough trouble with just the one!

There's no way to make the metal ion show up. It really is missing.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons