Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils.

@article{Zhang2010OptimalAS,
  title={Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils.},
  author={Jiapu Zhang and Jie Sun and Changzhi Wu},
  journal={Journal of theoretical biology},
  year={2010},
  volume={279 1},
  pages={
          17-28
        }
}
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15 Citations
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Methods Citations
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Results Citations
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15 Citations

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The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils

A new theoretical computational method is presented—an improved LBFGS Quasi-Newtonian mathematical optimization method—to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view.

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The hybrid idea of optimization methods is effective, necessary and efficient for solving the potential energy minimization problem and the Lennard-Jones clusters problem and an application to prion protein structures is done by the hybrid idea.

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References

SHOWING 1-10 OF 151 REFERENCES

Optimal molecular structures of prion AGAAAAGA amyloid fibrils formatted by simulated annealing

The successful construction of three amyloid fibril models for the AGAAAAGA palindrome in the hydrophobic region of prion proteins are reported, which confirm standard simulated annealing as an effective tool in molecular modeling.

Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential

Using the microcrystal structure of the NNQQNY peptide from yeast prion protein and residue-based statistical potentials to establish an algorithm to identify the amyloid fibril-forming segment of proteins agrees with the idea that peptides that can form fibrils may have strong sequence signatures.

Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35.

Simulations show that with the increase in the number of strands even from a dimer to a trimer, oligomer stability increases dramatically, and suggests that the minimal nucleus seed for GNNQQNY fibril formation could be small and is likely three or four peptides, and that higher-order oligomers do not dissociate quickly since they have small diffusion coefficients and thus slow kinetics.

Atomic structures of amyloid cross-β spines reveal varied steric zippers

Structures of 13 of these microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.

NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106–126

Fibril formation involving polyalanine stacking is consistent with the experimental observations, and molecular dynamics simulations indicate that MoPrP106–126 in water assumes a stable structure consisting of two four-stranded parallel β-sheets that are tightly packed against each other by methyl–methyl interactions.

A Model for Structure-Dependent Binding of Congo Red to Alzheimer β-Amyloid Fibrils

The Hydrophobic Core Sequence Modulates the Neurotoxic and Secondary Structure Properties of the Prion Peptide 106‐126

Structural analyses show that the hydrophobic core sequence is important for PrP106‐126 toxicity probably by influencing its assembly into a neurotoxic structure, and may similarly affect aggregation and toxicity observed in prion diseases.

NMR structure of the mouse prion protein domain PrP(121–231)

The nuclear magnetic resonance (NMR) structure of the autonomously folding PrP domain contains most of the point-mutation sites that have been linked, in human PrP, to the occurrence of familial prion diseases, and shows that these mutations occur within, or directly adjacent to, regular secondary structures.

Studies on the structural stability of rabbit prion probed by molecular dynamics simulations of its wild-type and mutants.

  • Jiapu Zhang
  • Biology, Chemistry
    Journal of theoretical biology
  • 2010

Energy-optimized structure of antifreeze protein and its binding mechanism.

  • K. Chou
  • Chemistry
    Journal of molecular biology
  • 1992
...