Computational Potential Energy Minimization Studies on the Prion AGAAAAGA Amyloid Fibril Molecular Structures

Abstract

X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, and dual polarization interferometry, etc are indeed very powerful tools to determine the 3D structures of proteins (including the membrane proteins), though they are time-consuming and costly. However, for some proteins, due to their unstable, noncrystalline and insoluble nature, these tools cannot work. Under this condition, mathematical and physical theoretical methods and computational approaches allow us to obtain a description of the protein 3D structure at a submicroscopic level. This Chapter presents some practical and useful mathematical optimization computational approaches to produce 3D structures of the Prion AGAAAAGA Amyloid Fibrils, from a potential energy minimization point of view. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements in order to produce a better structure. The computational methods presented in this Chapter can be also acted as a tool for the refinements.