Secondary Structure in Amyloids in Relation to Their Wild Type Forms

The amyloid structures and their wild type forms, available in the PDB database, provide the basis for comparative analyses. Globular proteins are characterised by a 3D spatial structure, while a chain in any amyloid fibril has a 2D structure. Another difference lies in the structuring of the hydrogen bond network. Amyloid forms theoretically engage all the NH and C=O groups of the peptide bonds in a chain with two hydrogen bonds each. In addition, the hydrogen bond network is highly ordered-as perpendicular to the plane of the chain. The beta-structure segments provide the hydrogen bond system with an anti-parallel system. The folds appearing in the rectilinear propagation of the segment with the beta-structure are caused by just by one of the residues in the sequence-residues with a R alpha-helical or L alpha-helical conformation. The antiparallel system of the hydrogen bonds in the beta-structure sections at the site of the amino acid with a R alpha- or L alpha-helical conformation changes into a parallel system locally. This system also ensures that the involvement of the C=O and H-N groups in the construction of the interchain hydrogen bond, while maintaining a perpendicular orientation towards the plane of the chain. Conformational analysis at the level of the Phi and Psi angles indicates the presence of the conditions for the structures observed in the amyloids. The specificity of amyloid structures with the dominant conformation expressed as |Psi| = |Phi| reveals the system of organisation present in amyloid fibrils. The Phi, Psi angles, as present in this particular structure, transformed to form |Psi| = |Phi| appear to be ordered co-linearly. Therefore, the calculation of the correlation coefficient may express the distribution around this idealised localisation on the Ramachandran map. Additionally, when the outstanding points are eliminated, the part of amyloid chain can be classified as fulfilling the defined conditions. In addition, the presentation of the chain structure using geometric parameters, V-angle-the angle between the planes of the adjacent peptide bonds (angle versus the virtual axis C alpha-C alpha) and the radius of the curvature R, depending on the size of the angle V, allows for a quantitative assessment of changes during amyloid transformation.

Automated summary

The amyloid structures in the PDB database are compared with their wild type forms. Amyloid fibrils have a 2D structure and a different hydrogen bond network compared to globular proteins. The beta-structure segments in amyloid fibrils have an anti-parallel system of hydrogen bonds. The conformational analysis of Phi and Psi angles reveals the presence of specific conditions and the correlation coefficient can indicate the distribution on the Ramachandran map.