Hello,
My peptide is 20 residues long and it has been experimentally shown that this peptide( forms a helix in its native form) is sufficient for binding to a different protein. This peptide is attached to the other part of the protein via a loop and it is believed that this loop stabilizes the helix to some extent (the truncated helix is structurally unstable). For the experimental work, the stability of the helix is achieved by installing all-hydrocarbon staples on two residues at i and i+4 position.
I am trying to conduct peptide-protein docking analysis for the same. In what way/s can I stabilize the peptide before docking to achieve a good result? Your help will be appreciated.
Thanks, Khushboo
Hi Pritam,
Do you mean that the energy minimisation of the peptide should be done before docking? The reason being that I will be doing MD simulation of the complex (peptide and the protein) after docking.
Thanks a lot for your quick response.
Hi,
You can also perform MD simulation of the peptide to stabilize it and then you can go for docking. Hope this helps
Regards
Artificial alpha helix stabilisation can be achieved by using artificial upper and lower distance constraints between helical hydrogen bond donor and acceptor atoms. You will probably want to minimise using the helix constraints prior to docking. These artificial constraints can be removed once docked. If the helix should be there, complementary interactions should help to keep it.
For an alpha helix
Upper limits donor --- acceptor
2.00Å H O
3.00Å N O
Lower limits donor --- acceptor
1.80Å H O
2.70Å N O
Dihedral angle constraints can also be included to regularise the alpha helix.
Phi = -60, Psi = -45
In this case you should run MD simulation before performing docking simulation. Try to run MD as long as you can. As a result, it is possible to obtain an stable helix to interact with the peptide.
Hi Pritam,
Thanks for you suggestions. I will definitely let you know if I figure out a way to do MD simulation of the complex.
- Badges
- Science topic