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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
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Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
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Prion protein conversion triggered by acidic condition: a molecular dynamics study through different force fields.

Helen Nathalia Thompson1, Claudia Elizabeth Thompson2, Rafael Andrade Caceres2

  • 1Departamento de Físico-Química, Instituto de Química, Universidade Federal do Rio Grande do Sul, 91501-970, Porto Alegre, Rio Grande do Sul, Brazil.

Journal of Computational Chemistry
|September 22, 2018
PubMed
Summary
This summary is machine-generated.

The choice of force field significantly impacts prion protein structural conversion simulations. Only GROMOS96 53A6 and AMBER99SB accurately model β-sheet formation at acidic pH, crucial for understanding prion diseases.

Keywords:
force fieldsmolecular dynamicspHprionsecondary structure

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Neuroscience

Background:

  • Prions cause fatal neurodegenerative diseases like BSE.
  • The structure of the disease-associated prion protein (PrPSc) is not fully understood.
  • Prion conversion mechanisms are studied using hypothetical beta-rich structures.

Purpose of the Study:

  • To systematically investigate the influence of six different force fields on prion protein structural conversion.
  • To assess how acidic and neutral pH conditions affect structural changes.
  • To identify reliable force fields for simulating prion protein dynamics.

Main Methods:

  • In silico simulation of Syrian hamster cellular prion protein.
  • Utilized six distinct force fields: GROMOS96 53a6, GROMOS96 43a1, AMBER99SB, AMBER99SB-ILDN, CHARMM27, and OPLS-AA/L.
  • Simulations were performed at both acidic and neutral pH.

Main Results:

  • Simulation outcomes showed a strong dependence on the chosen force field.
  • Only GROMOS96 53A6 and AMBER99SB successfully predicted high beta-sheet formation at acidic pH.
  • These two force fields also adequately reproduced neutral pH conditions.
  • Beta-sheet elongation was observed to be driven by the N-terminal tail's movement towards the HB alpha-helix under acidic conditions.

Conclusions:

  • The selection of force fields is critical for accurate prion protein structural conversion modeling.
  • GROMOS96 53A6 and AMBER99SB are recommended for simulating acidic pH-induced structural changes in prion proteins.
  • This study provides a comprehensive comparison of force fields for prion protein structural dynamics.