88 research outputs found
Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides
We present an extension of the coarse-grained MARTINI
model for
proteins and apply this extension to amyloid- and elastin-like peptides.
Atomistic simulations of tetrapeptides, octapeptides, and longer peptides
in solution are used as a reference to parametrize a set of pseudodihedral
potentials that describe the internal flexibility of MARTINI peptides.
We assess the performance of the resulting model in reproducing various
structural properties computed from atomistic trajectories of peptides
in water. The addition of new dihedral angle potentials improves agreement
with the contact maps computed from atomistic simulations significantly.
We also address the question of which parameters derived from atomistic
trajectories are transferable between different lengths of peptides.
The modified coarse-grained model shows reasonable transferability
of parameters for the amyloid- and elastin-like peptides. In addition,
the improved coarse-grained model is also applied to investigate the
self-assembly of β-sheet forming peptides on the microsecond
time scale. The octapeptides SNNFGAIL and (GV)4 are used
to examine peptide aggregation in different environments, in water,
and at the water–octane interface. At the interface, peptide
adsorption occurs rapidly, and peptides spontaneously aggregate in
favor of stretched conformers resembling β-strands
Diversity Youth Forum Report
The volume gathers and discusses the contributions to the Diversity Youth Forum held by the Council of Europe in Budapest in October 2006 including both working group reports and lectures addressing issues of diversity, discrimination and youth policies and participation in Europe
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