The structural and dynamical behavior of the 41–56
β-hairpin from the protein G B1 domain (GB1) has been
studied at different temperatures using molecular dynamics
(MD) simulations in an aqueous environment. The purpose
of these simulations is to establish the stability of this
hairpin in view of its possible role as a nucleation site
for protein folding. The conformation of the peptide in
the crystallographic structure of the protein GB1 (native
conformation) was lost in all simulations. The new equilibrium
conformations are stable for several nanoseconds at 300
K (>10 ns), 350 K (>6.5 ns), and even at 450 K (up
to 2.5 ns). The new structures have very similar hairpin-like
conformations with properties in agreement with available
experimental nuclear Overhauser effect (NOE) data. The
stability of the structure in the hydrophobic core region
during the simulations is consistent with the experimental
data and provides further evidence for the role played
by hydrophobic interactions in hairpin structures. Essential
dynamics analysis shows that the dynamics of the peptide
at different temperatures spans basically the same essential
subspace. The main equilibrium motions in this subspace
involve large fluctuations of the residues in the turn
and ends regions. Of the six interchain hydrogen bonds,
the inner four remain stable during the simulations. The
space spanned by the first two eigenvectors, as sampled
at 450 K, includes almost all of the 47 different hairpin
structures found in the database. Finally, analysis of
the hydration of the 300 K average conformations shows
that the hydration sites observed in the native conformation
are still well hydrated in the equilibrium MD ensemble.