A novel canonical dual computational approach for prion AGAAAAGA amyloid fibril molecular modeling

DOI10.1016/J.JTBI.2011.06.024zbMATH Open1397.92548arXiv1107.4104OpenAlexW1984647787WikidataQ84490552 ScholiaQ84490552MaRDI QIDQ1786044FDOQ1786044

Authors: Jiapu Zhang, John Yearwood, David Y. Gao 

Publication date: 24 September 2018

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Abstract: Many experimental studies have shown that the prion AGAAAAGA palindrome hydrophobic region (113-120) has amyloid fibril forming properties and plays an important role in prion diseases. However, due to the unstable, noncrystalline and insoluble nature of the amyloid fibril, to date structural information on AGAAAAGA region (113-120) has been very limited. This region falls just within the N-terminal unstructured region PrP (1-123) of prion proteins. Traditional X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy experimental methods cannot be used to get its structural information. Under this background, this paper introduces a novel approach of the canonical dual theory to address the 3D atomic-resolution structure of prion AGAAAAGA amyloid fibrils. The novel and powerful canonical dual computational approach introduced in this paper is for the molecular modeling of prion AGAAAAGA amyloid fibrils, and that the optimal atomic-resolution structures of prion AGAAAAGA amyloid fibils presented in this paper are useful for the drive to find treatments for prion diseases in the field of medicinal chemistry. Overall, this paper presents an important method and provides useful information for treatments of prion diseases. Overall, this paper could be of interest to the general readership of Theoretical Biology.

Full work available at URL: https://arxiv.org/abs/1107.4104

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zbMATH Keywords

amyloid fibrilmathematical canonical duality optimization theorysensor network optimization problemstructural bioinformatics technologytwo-body theoretical physics

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20) Computational methods for problems pertaining to biology (92-08)

Cites Work

• Duality principles in nonconvex systems. Theory, methods and applications
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• Solving molecular distance geometry problems by global optimization algorithms
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• Global convergence of conjugate gradient methods without line search
• A stochastic/perturbation global optimization algorithm for distance geometry problems
• Predicting ion channels and their types by the dipeptide mode of pseudo amino acid composition
• Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils

Cited In (10)

• Molecular dynamics simulations of the full-length prion protein
• Molecular dynamics study of the fibril elongation of the prion protein fragment PrP106-126
• A canonical duality approach for the solution of affine quasi-variational inequalities
• Global optimal trajectory in chaos and NP-hardness
• Stable trajectory of logistic map
• Canonical duality for solving general nonconvex constrained problems
• \textit{In-silico} tuning of the nano-bio interface by molecular dynamics method: amyloid beta targeting with two-dimensional metal-organic frameworks
• Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils
• Canonical primal-dual algorithm for solving fourth-order polynomial minimization problems
• Studies on the structural stability of rabbit prion probed by molecular dynamics simulations of its wild-type and mutants

Uses Software

• VMD
• iLoc-Euk
• AFP-Pred

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