Computational and experimental studies on ß-sheet breakers targeting Aß1-40 fibrils.

In this work we present and compare the results of extensive molecular dynamics simulations of model systems comprising an Aß1-40 peptide in water in interaction with short peptides (ß-sheet breakers) mimicking the 17-21 region of the Aß1-40 sequence. Various systems differing in the customized ß-sheet breaker structure have been studied. Specifically we have considered three kinds of ß-sheet breakers, namely Ac-LPFFD-NH2 and two variants thereof, one obtained by substituting the acetyl group with the sulfonic amino acid taurine (Tau-LPFFD-NH2) and a second novel one in which the aspartic acid is substituted by an asparagine (Ac-LPFFN-NH2). Thioflavin T fluorescence, circular dichroism, and mass spectrometry experiments have been performed indicating that ß-sheet breakers are able to inhibit in vitro fibril formation and prevent the ß sheet folding of portions of the Aß1-40 peptide. We show that molecular dynamics simulations and far UV circular dichroism provide consistent evidence that the new Ac-LPFFN-NH2 ß-sheet breaker is more effective than the other two in stabilizing the native α-helix structure of Aß1-40. In agreement with these results thioflavin T fluorescence experiments confirm the higher efficiency in inhibiting Aß1-40 aggregation. Furthermore, mass spectrometry data and molecular dynamics simulations consistently identified the 17-21 Aß1-40 portion as the location of the interaction region between peptide and the Ac-LPFFN-NH2 ß-sheet breaker.

Copper-zinc cross-modulation in prion protein binding.

In this paper we report a systematic XAS study of a set of samples in which Cu(II) was progressively added to complexes in which Zn(II) was bound to the tetra-octarepeat portion of the prion protein. This work extends previous EPR and XAS analysis in which, in contrast, the effect of adding Zn(II) to Cu(II)-tetra-octarepeat complexes was investigated. Detailed structural analysis of the XAS spectra taken at both the Cu and Zn K-edge when the two metals are present at different relative concentrations revealed that Zn(II) and Cu(II) ions compete for binding to the tetra-octarepeat peptide by cross-regulating their relative binding modes. We show that the specific metal-peptide coordination mode depends not only, as expected, on the relative metal concentrations, but also on whether Zn(II) or Cu(II) was first bound to the peptide. In particular, it seems that the Zn(II) binding mode in the absence of Cu(II) is able to promote the formation of small peptide clusters in which triplets of tetra-octarepeats are bridged by pairs of Zn ions. When Cu(II) is added, it starts competing with Zn(II) for binding, disrupting the existing peptide cluster arrangement, despite the fact that Cu(II) is unable to completely displace Zn(II). These results may have a bearing on our understanding of peptide-aggregation processes and, with the delicate cross-regulation balancing we have revealed, seem to suggest the existence of an interesting, finely tuned interplay among metal ions affecting protein binding, capable of providing a mechanism for regulation of metal concentration in cells.