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 beta-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 beta-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 beta-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.

Automated summary

In this study, a folding molecular dynamics simulation was performed to investigate the structural and dynamical properties of Peptide T. The simulation revealed that Peptide T is flexible and dynamic, with a preference for the formation of beta-turns. The results were validated by comparing with experimental NMR data, showing a reasonable agreement between experiment and simulation. This study demonstrates that peptide folding simulations can provide physically relevant structural characterization.