Computational Potential Energy Minimization Studies on the Prion AGAAAAGA Amyloid Fibril Molecular Structures

Zhang, Jiapu

doi:10.5772/47733

Cited by 3 publications

(3 citation statements)

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“…Computer simulations of amyloid fibril formation by the Syrian hamster prion protein (SHaPrP) residues AGAAAAGA, the mouse prion protein (MoPrP) residues VA- GAAAAGAV, and their variations GA 6 G (a longer uninterrupted Alanine stretch flanked by Glycine), (AG) 4 (a complete disruption of hydrophobic residues), A 8 , GAAAGAAA (a mimic of Aβ (29)(30)(31)(32)(33)(34)(35)(36)), A 10 , V 10 , GAVAAAAVAG (uninterrupted hydrophobic sequence), VAVAAAAVAV (less flexible than MoPrP(111-120)) are studied in [10]. The first two peptides are thought to act as the velcro that holds the parent prion proteins together in amyloid structures and can form fibrils themselves [10].…”

Section: A Survey Of the Research Work On Agaaaagamentioning

confidence: 99%

“…In all these models, there is about 5 angstroms between the two closest adjacent β-sheets, maintained by hydrophobic bonds, and about 4.5 angstroms between the two closest adjacent β-strands, which are linked by hydrogen bonds. Illuminated by PDB templates 3FVA, 3NHC/D, 3NVF/G/H/E, 3MD4/5, 2OMP, computational approaches of global optimization, local search energy minimization (EM), simulated annealing (SA) and structural bioinformatics etc or introducing novel mathematical formulations and physical concepts into molecular biology may allow us to obtain a description of the protein 3D structure at a submicroscopic level for prion AGAAAAGA amyloid fibrils [24,26,27,28,29,30].…”

Section: D Structure Of Prion Agaaaaga Amyloid Fibrilsmentioning

confidence: 99%

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Molecular dynamics studies on 3D structures of the hydrophobic region PrP(109-136)

Zhang¹,

Zhang²

2013

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Prion diseases, traditionally referred to as transmissible spongiform encephalopathies, are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species, manifesting as scrapie in sheep, bovine spongiform encephalopathy (or 'mad-cow' disease) in cattle, and Creutzfeldt-Jakob disease, Gerstmann-Strussler-Scheinker syndrome, fatal familial insomnia (FFI), and Kulu in humans, etc. These neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein (PrP(C)) into insoluble abnormally folded infectious prions (PrP(Sc)). The hydrophobic region PrP(109-136) controls the formation of diseased prions: the normal PrP(113-120) AGAAAAGA palindrome is an inhibitor/blocker of prion diseases and the highly conserved glycine-xxx-glycine motif PrP(119-131) can inhibit the formation of infectious prion proteins in cells. This article gives detailed reviews on the PrP(109-136) region and presents the studies of its three-dimensional structures and structural dynamics.

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Section: A Survey Of the Research Work On Agaaaagamentioning

confidence: 99%

Section: D Structure Of Prion Agaaaaga Amyloid Fibrilsmentioning

confidence: 99%

Molecular dynamics studies on 3D structures of the hydrophobic region PrP(109-136)

Zhang¹,

Zhang²

2013

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“…Solving the ten MDGPs in the above section by any Optimization Solver (which will remove the bad vdW/HB contacts) [9][10][11][12][13][14][15][16] and then refining all the models by the Optimization program of Amber 11 [9,17]. At last we got the optimized prion 113-120 GAAAAGA amyloid fibril models, which are illuminated in Figures 8-14.…”

Section: Resultsmentioning

confidence: 99%

The Sensor Network in Molecular Structures of PrP(113-120) AGAAAAGA Amyloid Fibrils

Zhang¹

2014

J Comput Sci Syst Biol

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The problem of locating sensors in telecommunication networks is a distance geometry problem (DGP). In such a case, the positions of some sensors are known (which are called anchors) and some of the distances between sensors (which can or cannot be anchors) are known. The DGP is to locate the positions of all the sensors. Molecular DGP (MDGP) looks sensors as atoms and their telecommunication network as a molecule for the determination of its three-dimensional (3D) structure. This Chapter defines some sensor networks for determining molecular structures of PrP(113-120) AGAAAAGA amyloid fibrils, which are unstable, noncrystalline, insoluble and hard to be determined in NMR or X-ray experimental laboratories. The amyloid fibril structure is the common structure associated with some 20 neurodegenerative amyloid diseases (including Parkinson's, Alzheimer's, Huntington's, and Prions'), and other diseases such as Type II diabetes, etc. The sensor networks established in this Chapter will benefit the study of 3D molecular structures of all these diseases and will be useful in the research areas such as structural materials, computer-aided or structure-based drug design, and the computational theory of molecular dynamics, and quantum mechanics/molecular mechanics.

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The Hybrid Method of Evolutionary Computations with Simulated Annealing

Zhang

2015

Molecular Structures and Structural Dynamics of Prion Proteins and Prions

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Computational Potential Energy Minimization Studies on the Prion AGAAAAGA Amyloid Fibril Molecular Structures

Cited by 3 publications

References 61 publications

Molecular dynamics studies on 3D structures of the hydrophobic region PrP(109-136)

Molecular dynamics studies on 3D structures of the hydrophobic region PrP(109-136)

The Sensor Network in Molecular Structures of PrP(113-120) AGAAAAGA Amyloid Fibrils

The Hybrid Method of Evolutionary Computations with Simulated Annealing

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