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The Possible Mechanism of Amyloid Transformation Based on the Geometrical Parameters of Early-Stage Intermediate in Silico Model for Protein Folding

Authors: Irena Roterman; Katarzyna Stapor; Dawid Dułak; Leszek Konieczny;

The Possible Mechanism of Amyloid Transformation Based on the Geometrical Parameters of Early-Stage Intermediate in Silico Model for Protein Folding

Abstract

The specificity of the available experimentally determined structures of amyloid forms is expressed primarily by the two- and not three-dimensional forms of a single polypeptide chain. Such a flat structure is possible due to the β structure, which occurs predominantly. The stabilization of the fibril in this structure is achieved due to the presence of the numerous hydrogen bonds between the adjacent chains. Together with the different forms of twists created by the single R- or L-handed α-helices, they form the hydrogen bond network. The specificity of the arrangement of these hydrogen bonds lies in their joint orientation in a system perpendicular to the plane formed by the chain and parallel to the fibril axis. The present work proposes the possible mechanism for obtaining such a structure based on the geometric characterization of the polypeptide chain constituting the basis of our early intermediate model for protein folding introduced formerly. This model, being the conformational subspace of Ramachandran plot (the ellipse path), was developed on the basis of the backbone conformation, with the side-chain interactions excluded. Our proposal is also based on the results from molecular dynamics available in the literature leading to the unfolding of α-helical sections, resulting in the β-structural forms. Both techniques used provide a similar suggestion in a search for a mechanism of conformational changes leading to a formation of the amyloid form. The potential mechanism of amyloid transformation is presented here using the fragment of the transthyretin as well as amyloid Aβ.

Keywords

Amyloid, Protein Folding, $\beta$-structure, amyloid, amyloid; secondary structure; α-helix unfolding; β-structure; left-handed α-helix; hydrogen bonds; transthyretin; protein folding; early stage of folding; misfolding, secondary structure, Amyloidogenic Proteins, Hydrogen Bonding, Molecular Dynamics Simulation, misfolding, $\alpha$-helix unfolding, transthyretin, Article, left-handed $\alpha$-helix, protein folding, hydrogen bonds, early stage of folding, Peptides

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
3
Top 10%
Average
Average
Green
gold