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

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

Title
The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils
Creator
Zhang, Jiapu; Hou, Yating; Wang, Yiju; Wang, Changyu; Zhang, Xiangsun
Date
2012
Type
Text; Journal article
Identifier
http://researchonline.federation.edu.au/vital/access/HandleResolver/1959.17/67122
Identifier
vital:5112
Identifier
https://doi.org/10.4236/ns.2012.412A138
Identifier
ISSN:2150-4091
Abstract
Experimental X-ray crystallography, NMR (Nu- clear 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 introduc- es some optimization algorithms used in these research fields and presents a new theoretical computational method—An improved LBFGS Quasi-Newtonian mathematical optimization me- thod—to produce 3D structures of prion AGAA- AAGA amyloid fibrils (which are unstable, non-crystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic re-gion AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experi-mental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.
Relation
Natural Science Vol. 4, no. 12A (2012), p. 1097-1108
Rights
Copyright 2012 SciRes
Rights
Open Access
Rights
This metadata is freely available under a CCO license
Subject
Protein 3D structure; Computational
Full Text
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