normal D-amino acids

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9 years 3 months ago #4519 by jseco
D-amino acids was created by jseco
Hello to everybody,

I'm a newbie in Martini Force Field and I would like to apply to my research, mostly focused to understand based on first principles the folding of heterochiral peptides (i.e, L- and D- aminoacids in the same sequence)

I was wondering if anyone could just shed light on the feasiblity to successfully sample with Martini FF the conformational space of such peptides, as the only difference between any L- and D- amino acid is their miror image values for phi and psi torsional angles. Is possible to incorporate such information into the bead of the aminoacid ?

Thanks in advance!

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9 years 3 months ago #4524 by Pim
Replied by Pim on topic D-amino acids
Sadly, the peptide chirality is 'coarse-grained out' in the Martini force field. If you really want to 'create' a difference you can try to parameterise a potential that keeps e.g. an improper dihedral on the backbone bead around a certain value by fitting an atomistic simulation.

For parameterising advanced backbone dihedrals in martini, see www.ncbi.nlm.nih.gov/pmc/articles/PMC3348680/
For an example of a study that uses D-peptides (but uses identical parameters as for the L-amino acids), see pubs.rsc.org/en/content/articlehtml/2014/cp/c3cp53101e

Good luck!

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9 years 3 months ago #4526 by jseco
Replied by jseco on topic D-amino acids
Many thanks for the info, I was pretty aware about those coarse-grained limitations but I honestly hoped there could an easier way to solve this issue.

I will take a look to those journals and in case positive results arise, I will share with Maritini's community.

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