Peldor Beyond Distances

Long-Range Distances in Amyloid Fibrils of a-Synuclein from PELDOR Spectroscopy**

Long-Range Distances in Amyloid Fibrils of α-Synuclein from PELDOR Spectroscopy**

a-Synuclein (aS), a small protein containing 140 amino acids, undergoes self-assembly into amyloid fibrils and plaques (Lewy bodies), which are pathological hallmarks of Parkinson s disease (PD) as well as other neurodegenerative diseases. While oligomeric species of aS are considered to exert the neurotoxic activity that can be rescued by reducing those oligomers either by diversion to smaller...

Measurements of short distances between trityl spin labels with CW EPR, DQC and PELDOR.

Trityl based spin labels are emerging as a complement to nitroxides in nanometer distance measurements using EPR methods. The narrow spectral width of the trityl radicals prompts us to ask the question at which distance between these spin centers, the pseudo-secular part of the dipolar coupling and spin density delocalization have to be taken into account. For this, two trityl-trityl and one tr...

Beyond Adjacency Maximization: Scaffold Filling for New String Distances

In Genomic Scaffold Filling, one aims at polishing in silico a draft genome, called scaffold. The scaffold is given in the form of an ordered set of gene sequences, called contigs. This is done by confronting the scaffold to an already complete reference genome from a close species. More precisely, given a scaffold S, a reference genome G and a score function f() between two genomes, the aim is...

Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates.

The "neighbor-joining algorithm" is a recursive procedure for reconstructing trees that is based on a transformation of pairwise distances between leaves. We present a generalization of the neighbor-joining transformation, which uses estimates of phylogenetic diversity rather than pairwise distances in the tree. This leads to an improved neighbor-joining algorithm whose total running time is st...