The Structural Stability of Wild-type Horse Prion Protein

Zhang, Jiapu

doi:10.1080/07391102.2011.10507391

Cited by 45 publications

(35 citation statements)

References 20 publications

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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%

“…First, we analyze the role of GSVVGGLGGYMLGSAMSR (PrP(119-136)) in horse PrP C (119-231) (PDB entry 2KU4). In our study [35], the MD simulation conditions are at 350 K in explicit solvent under neutral and low pH environments, heatings are using the Langevin thermostat algorithm in constant NVT ensembles and the equilibrations and productions are using Langevin thermostat algorithm in constant NPT ensembles. Seeing the Tables I-III of the Supplementary Material of [35], we know the following HBs of GSVVGGLGGYML-GSAMSR (PrP(119-136)):…”

Section: Molecules In This Parts Of the Truncated Octahedral Box Of Tmentioning

confidence: 99%

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

Zhang¹,

Zhang²

2013

ABBS

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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: Molecules In This Parts Of the Truncated Octahedral Box Of Tmentioning

confidence: 99%

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

Zhang¹,

Zhang²

2013

ABBS

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“…4, we may know that at the S2-H2 loop it is mainly covered by the electrical cloud of negatively (in red color) charged residues [except for mousePrP[D167S,N173K], rabbitPrP-NMR and horsePrP etc (Fig. 2)], with positively (in blue) charged residues R164 (for all species) and H177 (for mousePrP, humanPrP-M129, mousePrP[D167S,N173K] only) at the N-terminal end and C-terminal end of S2-H2 loop respectively (we found there is a salt bridge R164-D178 linking this loop of rabbitPrP-NMR, rabbitPrP-X-ray, horsePrP, dogPrP, elkPrP and buffaloPrP for long time MD simulations [57,61,62,69,74,72,66,63]). From Tab.…”

Section: The Hybrid Idea and Some Hybrid Optimization Methodsmentioning

confidence: 88%

The Hybrid Idea of (Energy Minimization) Optimization Methods Applied to Study PrionProtein Structures Focusing on the beta2-alpha2 Loop

Zhang¹

2015

Biochem Pharmacol (Los Angel)

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In molecular mechanics, current generation potential energy functions provide a reasonably good compromise between accuracy and effectiveness. This paper firstly reviewed several most commonly used classical potential energy functions and their optimization methods used for energy minimization. To minimize a potential energy function, about 95% efforts are spent on the Lennard-Jones potential of van der Waals interactions; we also give a detailed review on some effective computational optimization methods in the Cambridge Cluster Database to solve the problem of Lennard-Jones clusters. From the reviews, we found the hybrid idea of optimization methods is effective, necessary and efficient for solving the potential energy minimization problem and the Lennard-Jones clusters problem. An application to prion protein structures is then done by the hybrid idea. We focus on the β2-α2 loop of prion protein structures, and we found (i) the species that has the clearly and highly ordered β2-α2 loop usually owns a 3 10 -helix in this loop, (ii) a "π-circle" Y128-F175-Y218-Y163-F175-Y169-R164-Y128(-Y162) is around the β2-α2 loop.

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“…Comparing with human prion protein, the rabbit prion protein has stable molecular dynamical structure under neutral PH environment, but dog and horse prion proteins have stable molecular dynamical structures under neutral or low PH environments. 16,18,19 In experiments where no cases of prion diseases were reported for horses. 20 These prion diseases were caused by the conversion from normal PrP C to abnormally folded PrP Sc , so these diseases were called protein \structural conformational" diseases.…”

Section: à14mentioning

confidence: 99%

COMPARING FOLDING MECHANISMS OF DIFFERENT PRION PROTEINS BY Gō MODEL

吴雪

Xiu

et al. 2013

J. Theor. Comput. Chem.

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Prions are associated with neurodegenerative diseases induced by transmissible spongiform encephalopathies. The infectious scrapie form is referred to as PrP Sc , which has conformational change from normal prion with predominant -helical conformation to the abnormal PrP Sc that is rich in -sheet content. Neurodegenerative diseases have been found from both human and bovine sources, but there are no reports about infected by transmissible spongiform encephalopathies from rabbit, canine and horse sources. Here we used coarse-grained Gō model to compare the di®erence among human, bovine, rabbit, canine, and horse normal (cellular) prion proteins. The denatured state of normal prion has relation with the conversion from normal to abnormal prion protein, so we used all-atom Gō model to investigate the folding pathway and energy landscape for human prion protein. Through using coarse-grained Gō model, the cooperativity of the¯ve prion proteins was characterized in terms of calorimetric criterion, sigmoidal transition, and free-energy pro¯le. The rabbit and horse prion proteins have higher folding free-energy barrier and cooperativity, and canine prion protein has slightly higher folding free-energy barrier comparing with human and bovine prion proteins. The results from † † Corresponding authors.Journal of Theoretical and Computational Chemistry Vol. 12, No. 8 (2013) all-atom Gō model con¯rmed the validity of C -Gō model. The correlations of our results with previous experimental and theoretical researches were discussed.

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The Structural Stability of Wild-type Horse Prion Protein

Cited by 45 publications

References 20 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 Hybrid Idea of (Energy Minimization) Optimization Methods Applied to Study PrionProtein Structures Focusing on the beta2-alpha2 Loop

COMPARING FOLDING MECHANISMS OF DIFFERENT PRION PROTEINS BY Gō MODEL

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