normal Martinize and uncharged lysine side chain

  • danijoo
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7 years 6 months ago #5872 by danijoo
Hello,

Im trying to martinize a membrane protein structure that explicitly has to bear an uncharged lysine residue. When feeding the PDB bearing the unprotonated lysine into martinize, it still generates an .itp with the charged lysine residue (mapping C3-Qd instead of C3-P1).

Im trying to make the changes to the .itp manually but I am new to this. Is it correct that exchanging the Bead type (Qd to P1) and changing the charge sufficent for that change. From the paper the mapping scheme for Qd and P1 seems to be the same for lysine.

Best regards,
Daniel B

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7 years 6 months ago #5889 by peterkroon
Replied by peterkroon on topic Martinize and uncharged lysine side chain
Hi Daniel,

first off, are you absolutely sure your lysine is uncharged?
The changes you'll need to make in your itp file are indeed the bead type and the charge.
The beadtype should be set to Nd ( dx.doi.org/10.1021/jp071097f ), and the charge should be 0.

Good luck!

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7 years 6 months ago - 7 years 6 months ago #5894 by danijoo
Replied by danijoo on topic Martinize and uncharged lysine side chain
Hello,

yes im sure it has to be uncharged. Im working on potassium channels and previous studies showed the uncharged lysine residue is crucial for channel current.

Why do you think it should be Nd and not P1? From the paper about the protein extension on MARTINI it says the assignment for lysine is C3-Qd for charged and C3-P1 for uncharged lysine (dx.doi.org/10.1021/ct700324x). (Although I have to admit that I'd also expected a donor type bead instead of polar)

Thanks!
Last edit: 7 years 6 months ago by danijoo.

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7 years 6 months ago #5901 by peterkroon
Replied by peterkroon on topic Martinize and uncharged lysine side chain
Hi,

You are correct, it should be P1. I just looked up an aliphatic primary uncharged amine in the original Martini paper. Apparently this is not completely transferrable to amino acids.

Good luck!

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