  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.
