normal Peptide aggregation

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1 year 4 months ago #8052 by pela3247
Peptide aggregation was created by pela3247
Hi,

We are currently running a series of simulations with the aim of studying peptide aggregation with the Martini forcefield. We have three peptides, for which we know the aggregation propensities based on so-called critical aggregation concentrations.

Currently, we have done one simulation of each peptide at a concentration of 1 mM, but the results when looking at aggregation show a reverse trend compared to literature data. i.e. the peptide which should aggregate the least seems to be aggregating the most.

I am curious to discuss the reasons for this! The peptides contain 9 residues each, some of which are non-natural and we have had to make some modifications based on the closest natural amino acid. But aside for potential errors in these modification, what could other reasons be? I have read the recent literature about excessive aggregation for sugars etc., but don't think that plays a significant role here? All simulations are without polarizable water, if it is relevant?

Thanks
/Per

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1 year 4 months ago #8053 by Pim
Replied by Pim on topic Peptide aggregation
Hi Per,
First of all, which Martini version are you using? It sounds like 2.2, but results will be different with 2.2P or 3, so it's important and it might be worth a try to use the latest version.

Although in 2.2 aromatic interactions were already lowered (de Jong et al paper on dimerization of side chains), it was possible that aromatic residues attracted each other a little too much.

Other reasons could be the choice for your backbone. Did you give any secondary structure when you martinized your peptide? For 9 residue-long peptides this might be quite important (and difficult to optimize). All coil seems a logical choice, but all coil backbones are different (all P5) than e.g. beta-sheet backbones (Nda) for Martini 2, and elastic bonds might be added to keep the peptide straight. For longer peptides, we found a few strange results with Martini if we didn't add any backbone dihedrals to keep the "secondary structure". What was your choice? Does your itp file have elastic bonds or did you remove them?

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