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Structure and dynamics of two beta-peptides in solution from molecular dynamics simulations validated against experiment

We have studied two different beta-peptides in methanol using explicit solvent molecular dynamics simulations and the GROMOS 53A6 force fi eld: a heptapeptide (peptide 1) expected to form a left-handed 314-helix, and a hexapeptide (peptide 2) expected to form a beta-hairpin in solution. Our analysis has focused on identifying and analyzing the stability of the dominant secondary structure conformations adopted by the peptides, as well as on comparing the experimental NOE distance upper bounds and 3J-coupling values with their counterparts calculated on the basis of the simulated ensembles. Moreover, we have critically compared the present results with the analogous results obtained with the GROMOS 45A3 (peptide 1) and 43A1 (peptide 2) force fi elds. We conclude that within the limits of conformational sampling employed here, the GROMOS 53A6 force fi eld satisfactorily reproduces experimental fi ndings regarding the behavior of short beta-peptides, with accuracy that is comparable to but not exceeding that of the previous versions of the force fi eld.

beta-peptides; molecular dynamics

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