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Sawaya, M.R., Sambashivan, S., Nelson, R., Ivanova, M.I., Sievers, S.A., Apostol, M.I., Thompson, M.J., Balbirnie, M., Wiltzius, J.J., McFarlane, H.T., Madsen, A., Riekel, C. and Eisenberg, D. (2007) Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature, 447, 453-457. doi:10.1038/nature05695

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

  AUTHORS: Jiapu Zhang, Yating Hou, Yiju Wang, Changyu Wang, Xiangsun Zhang

  KEYWORDS: Protein 3D Structure; Computational Approaches; Optimization Method; Molecular Modelling; Prion AGAAAAGA Amyloid Fibrils

  JOURNAL NAME: Natural Science, Vol.4 No.12A, December 31, 2012

  ABSTRACT: Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein); theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method—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. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.