Create disulfide bridges in a molecule
Instructions
To add a protein sequence with disulfide bridges to a project do the following:
Use M: Molecule: Molecules and enter the {Add Sequence} tab. Set “Polymer Type:” to protein and add the sequence in the ‘Sequence Input’ field. Set “Destination Mol System:” to "<None>". The Molecular System should not be set at this stage, because as soon as a Molecular system has been created, the molecule will be locked and no more changes can be made to it or to its links. Click [Add Sequence!] to create a new molecule with the entered sequence.
Enter {Sequences} and choose “link:SG” in the editable table cells of of the actual Cysteines that need to be linked under |Desciptor & Stereochemistry| (see figure below). The selected Cysteines can now be linked to one another.
Enter {Links} and select the molecule in “Molecule:” under ‘Intra Molecule Links’. Select a Cys to link from in “Source Residue:” and select a Cys to link to under |Destination Residue| (see figure below). A disulfide bridge has now been set between the two residues.
After the molecule template has been created, we can translate it into a molecule and create the associated chain and molecular system. To do this go to {Chains}, select the molecule template in “Template for new chain:” and click [Make Chain From Template]:
Command flowchart
M: Molecule: Molecules
{Add Sequence}
Set “Polymer Type:” to protein and enter the sequence
Set “Destination Mol System:” to [<None>]
Click [Add Sequence!]
{Sequences}
Choose “link:SG” in the editable table cells of of the actual Cysteines
{Links}
Select the molecule in “Molecule:” under ‘Intra Molecule Links’
Select a Cys to link from in “Source Residue:”
Select a Cys to link to under |Destination Residue|
Chains
Select the molecule template in “Template for new chain:” and click [Make Chain From Template]