Folding Molecular Dynamics Simulation of a gp41-Derived Peptide Reconcile Divergent Structure Determinations

Folding molecular dynamics simulation of T-peptide, a HIV viral entry inhibitor: Structure, dynamics, and comparison with the experimental data

Peptide T is a synthetic octapeptide fragment, which corresponds to the region 185-192 of the gp120 HIV coat protein and functions as a viral entry inhibitor. In this work, a folding molecular dynamics simulation of peptide T in a membrane-mimicking (DMSO) solution was performed with the aim of characterizing the peptide's structural and dynamical properties. We show that peptide T is highly flexible and dynamic. The main structural characteristics observed were rapidly interconverting short helical stretches and turns, with a notable preference for the formation of β-turns. The simulation also indicated that the C-terminal part appears to be more stable than the rest of the peptide, with the most preferred conformation for residues 5-8 being a β-turn. In order to validate the accuracy of the simulations, we compared our results with the experimental NMR data obtained for the T-peptide in the same solvent. In agreement with the simulation, the NMR data indicated the presence of a preferred structure in solution that was consistent with a β-turn comprising the four C-terminal residues. An additional comparison between the experimental and simulation-derived chemical shifts also showed a reasonable agreement between experiment and simulation, further validating the simulation-derived structural characterization of the T-peptide. We conclude that peptide folding simulations produce physically relevant results even when performed with organic solvents that were not part of the force field parameterization procedure.

A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations

Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 μs each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations within the DFT framework have shown that these peptides adopt β-turn structures in aqueous solution, with type I’ β-turn being the most preferred motif. The results from our analyses indicate that at least for the given systems, force field and simulation protocol, the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.