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

The EU's Political Conditionality and Post-Accession Tendencies: Comparisons from Slovakia and Latvia

The EU's political conditionality during the 2004 enlargement process recorded significant progress but imperfect implementation. But what has happened since post-Communist countries joined the EU three years ago now that the leverage of Brussels has ceased? This article develops an analytical approach to answer this question and applies it to the two cases of Slovakia and Latvia during the first three years of membership, showing some further progress with conditionality matters but also a rather mixed picture. Altogether, there is no common pattern whereby conditionalty loses momention and becomes unscrambled even though the drive behind enlargement has been the crucial force driving conditionality policy. Copyright (c) 2008 The Author(s).