Comparison of the structure of Aβ(1-40) amyloid with the one in complex with polyphenol ε-viniferin glucoside (EVG)

Abstract The analysis of amyloid structures is much easier recently due to the availability of the solid-state nuclear magnetic resonance technique, which allows the determination of the 3D structure of amyloid forms. The amyloidogenic polypeptide Aβ(1-40) (PDB ID 2M9R, 2M9S) in its soluble form is the object of analysis in this paper. The solubility of this polypeptide is reached due to the presence of a complexed ligand: polyphenol ε-viniferin glucoside. Two forms of complexes available in the PDB were taken for analysis with respect to the presence of a hydrophobic core in the 3D structure of these complexes. The idealized hydrophobic core structure assumed to be accordant with the 3D Gauss function distribution was taken as the pattern. The aim of this analysis is the possible further comparison to the structures of the hydrophobic core present in amyloids. It is shown that the discordant (versus the 3D Gauss function) fragments present in amyloids appear accordant in the discussed complexes.

[1]  R. A. Leibler,et al.  On Information and Sufficiency , 1951 .

[2]  C. Dobson,et al.  Protein folding and misfolding inside and outside the cell , 1998, The EMBO journal.

[3]  G Taubes,et al.  Protein Chemistry: Misfolding the Way to Disease , 1996, Science.

[4]  M. Levitt.  A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.

[5]  Arthur L Horwich,et al.  Deadly Conformations—Protein Misfolding in Prion Disease , 1997, Cell.

[6]  R. L. Baldwin.  The nature of protein folding pathways: The classical versus the new view , 1995, Journal of biomolecular NMR.

[7]  I. Roterman,et al.  Towards the design of anti-amyloid short peptide helices , 2018, Bioinformation.

[8]  R. Petersen,et al.  Interaction between amyloidogenic proteins and biomembranes in protein misfolding diseases: Mechanisms, contributors, and therapy. , 2018, Biochimica et biophysica acta. Biomembranes.

[9]  R. Jaenicke.  Folding and association versus misfolding and aggregation of proteins. , 1998, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[10]  Irena Roterman-Konieczna,et al.  Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins , 2015, Entropy.

[11]  Alan C. Evans,et al.  Mathematical Modeling of Protein Misfolding Mechanisms in Neurological Diseases: A Historical Overview , 2018, Front. Neurol..

[12]  P. Conn,et al.  Pharmacoperones as Novel Therapeutics for Diverse Protein Conformational Diseases. , 2018, Physiological reviews.

[13]  K. Nilsson,et al.  Amyloid fibril polymorphism: a challenge for molecular imaging and therapy , 2018, Journal of internal medicine.

[14]  Irena Roterman-Konieczna,et al.  Application of the Fuzzy Oil Drop Model Describes Amyloid as a Ribbonlike Micelle , 2017, Entropy.

[15]  I. Roterman,et al.  Propagation of Fibrillar Structural Forms in Proteins Stopped by Naturally Occurring Short Polypeptide Chain Fragments , 2017, Pharmaceuticals.

[16]  T. Richard,et al.  3D NMR structure of a complex between the amyloid beta peptide (1-40) and the polyphenol ε-viniferin glucoside: implications in Alzheimer's disease. , 2013, Biochimica et biophysica acta.

[17]  J. Baum,et al.  Folding of peptide models of collagen and misfolding in disease. , 1999, Current opinion in structural biology.

[18]  Bernardino Ghetti,et al.  Molecular subtypes of Alzheimer’s disease , 2018, Scientific Reports.

[19]  S. Ribaric.  Peptides as Potential Therapeutics for Alzheimer’s Disease , 2018, Molecules.

[20]  Irena Roterman-Konieczna,et al.  Influence of the Aqueous Environment on Protein Structure - A Plausible Hypothesis Concerning the Mechanism of Amyloidogenesis , 2016, Entropy.

[21]  Irena Roterman-Konieczna,et al.  Gauss-Function-Based Model of Hydrophobicity Density in Proteins , 2006, Silico Biol..