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Molecular Structures and Structural Dynamics of Prion Proteins and Prions pp 203–218Cite as

Hybrid Method of Discrete Gradient with Simulated Annealing or Genetic Algorithm

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Part of the book series: Focus on Structural Biology ((FOSB,volume 9))

Abstract

X-ray crystallography is a powerful tool to determine the protein 3D structure. However, it is time-consuming and expensive, and not all proteins can be successfully crystallized, particularly for membrane proteins. Although NMR spectroscopy is indeed a very powerful tool in determining the 3D structures of membrane proteins, it is also time-consuming and costly. To the best of the author’s knowledge, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113–120) of prion proteins due to the noncrystalline and insoluble nature of the amyloid fibril, although many experimental studies have shown that this region has amyloid fibril forming properties and plays an important role in prion diseases. In view of this, the present study is devoted to address this problem from computational approaches such as global energy optimization, simulated annealing, and structural bioinformatics. The optimal atomic-resolution structures of prion AGAAAAGA amyloid fibils reported in this chapter have a value to the scientific community in its drive to find treatments for prion diseases.

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    Jiapu Zhang

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Zhang, J. (2015). Hybrid Method of Discrete Gradient with Simulated Annealing or Genetic Algorithm. In: Molecular Structures and Structural Dynamics of Prion Proteins and Prions. Focus on Structural Biology, vol 9. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-7318-8_12

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