I have designed a peptide, carried out its simulation in normal saline using GROMACS and found increase in radius of gyration, along with Trace of the covariance matrix after diagonalizing around 9.0, increased RMSD value to around 3 Angstroms and mean RMSF of all amino acid in the sequence to be around 1.5 Angstroms.
Does all this data any how correlates with the cell penetrating property of a peptide?
If no, what all should I do to make the things more relevant?
Do any one can suggest me how to carry out simulation for cell penetrating property of a peptide taking lipid bilayer into consideration??
None of those metrics say anything about the ability penetrate a cell membrane.
If you want to study peptide-membrane interactions, you'll have to do simulations in the presence of a membrane, ideally unbiased binding. There is a large amount of literature on this topic regarding antimicrobial peptides, melittin, amyloid, etc.
I agree with Justin's answer. Cell membrane permeability of peptides depends on several factor such as amino acid composition, flexibility, conformation and length. It will good if you keep peptide outside the membrane and see its binding and penetration event in course of simulation.
I think one also should take into account the transmembrane potential gradient. A nice way to do it is using a double bilayer and asymmetric salt solutions. See for example.
Lee, Sun-Joo, Yuhua Song, and Nathan A. Baker. "Molecular Dynamics Simulations of Asymmetric NaCl and KCl Solutions Separated by Phosphatidylcholine Bilayers: Potential Drops and Structural Changes Induced by Strong Na< sup>+-Lipid Interactions and Finite Size Effects." Biophysical journal 94, no. 9 (2008): 3565-3576.
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