- Posts: 40
Phe Stacking
- nanogod
-
Topic Author
- Offline
- Senior Boarder
Less
More
11 years 5 months ago #1267
by nanogod
Phe Stacking was created by nanogod
Hey,
I am currently trying to run simulations with peptides where Phe stacking is part of the peptide-petide interaction. Hence, I would like to know if this stacking interaction is accounted for in the martini 2.2P force field or if I would have to optimize the LJ interaction for Phe?
From the article listed belov, I get the impression that Phe stacking was incorporated in martini version 2.1, but I have some doubts about if the self-assembly in this simulation is governed by electrostatic interactions rather than stacking effects.
pubs.acs.org/doi/abs/10.1021/nn300015g
Thank you in advance for your help
/Nanogod
I am currently trying to run simulations with peptides where Phe stacking is part of the peptide-petide interaction. Hence, I would like to know if this stacking interaction is accounted for in the martini 2.2P force field or if I would have to optimize the LJ interaction for Phe?
From the article listed belov, I get the impression that Phe stacking was incorporated in martini version 2.1, but I have some doubts about if the self-assembly in this simulation is governed by electrostatic interactions rather than stacking effects.
pubs.acs.org/doi/abs/10.1021/nn300015g
Thank you in advance for your help
/Nanogod
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
11 years 5 months ago #1272
by djurre
Replied by djurre on topic Phe Stacking
We recently looked at the dimerization of amino acid side chains (de Jong et al., J. Chem. Theory Comput, 2012, 8, 1003−1014). The interactions between two Phe side-chains was slightly to strong, which has been fixed by switching from SC4 to SC5 beads in Martini 2.2 (not yet published, but you in the martinize.py script the parameters have been implemented).
In that same paper we also looked at the orientation between different side chains and compared it to the orientation sampled by Gromos and OPLS. We did not look at Phe-Phe, but at a few other aromatics (also Phe-His). In general you can see (SI) that Martini does not approach as close as the atomistic force fields. The stacked orientation is sampled in a comparable amount as in the atomistic simulations.
In that same paper we also looked at the orientation between different side chains and compared it to the orientation sampled by Gromos and OPLS. We did not look at Phe-Phe, but at a few other aromatics (also Phe-His). In general you can see (SI) that Martini does not approach as close as the atomistic force fields. The stacked orientation is sampled in a comparable amount as in the atomistic simulations.
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
11 years 5 months ago #1279
by djurre
Replied by djurre on topic Phe Stacking
Hmmm, I should know my own work better. We did also look at the stacking of Phe-Phe pairs, however it is in the main text of [de Jong et al., J. Chem. Theory Comput, 2012, 8, 1003−1014]. We compared the stacking in water to OPLS and Gromos. Martini shows a pattern very similar to OPLS. Gromos has a lower tendency to have flat ring stacking. Also in more apolar solvents (octanol and decane) the binding patterns are similar.
BTW, the Martini 2.2 paper is also out by now: [DOI: 10.1021/ct300646g]
BTW, the Martini 2.2 paper is also out by now: [DOI: 10.1021/ct300646g]
Please Log in or Create an account to join the conversation.
Time to create page: 0.130 seconds