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

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

Centre for Informatics and Applied Optimization & Graduate School of Sciences, Information Technology and Engineering, The University of Ballarat, Victoria, Australia;.
Institute of Applied Mathematics, Academia Sinica, Beijing, China.
School of Management Science, Qufu Normal University, Rizhao, China.

DOI: 10.4236/ns.2012.412A138                

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.

Keywords

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

Conflicts of Interest

The authors declare no conflicts of interest.

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