On the Possible Spatial Structures of the β-Amyloid: The Native Structure of Proteins

On the Possible Spatial Structures of the β-Amyloid: The Native Structure of Proteins

Gennadiy Vladimirovich Zhizhin
DOI: 10.4018/IJARPHM.290380
OnDemand:
(Individual Articles)
Available
$37.50
No Current Special Offers
TOTAL SAVINGS: $37.50

Abstract

Spatial models of the β - structures of protein molecules, forming layers of amino acids, in principle, of unlimited length for both antiparallel and parallel conformation have been constructed. It is shown that the simplified flat Pauling models do not reflect the spatial structure of these layers. Using the recently developed theory of higher-dimensional polytopic prismahedrons, models of the volumetric filling of space with amino acid molecules are constructed. The constructed models for the first time mathematically describe the native structures of globular proteins.
Article Preview
Top

Introduction

Deposits of extracellular fibrillar proteins are the cause of serious diseases of the nervous system. The deposits are composed of amyloid, forming large aggregates with a β - structure (plaques). Plaques interfere with the functioning of nerve cells and cause various diseases: Alzheimer's, Parkinson's, Kreietzfeld-Jakob's and others (Koolman & Roehm, 2020). The patterns of development of these (prion) diseases and methods of their treatment are still poorly understood. The structure of "plaques" and the process of their formation also require deeper research. The indications that the "plaques" have a layered structure are insufficient to understand the issue. The concept of the layered structure of protein molecules as one of the protein conformations was introduced in the works of Pauling et al. (Pauling & Corey, 1950; Pauling, et al., 1951; Pauling & Corey, 1953; Corey & Pauling, 1953). In these works, it is assumed that the atoms of the peptide group connecting two amino acid residues are located in a plane. This assumption leads to the idea that protein molecules in this conformation form flat sheets, passing one into the other. Several publications claim that Pauling's model was the result of an analysis of experimental protein diffraction patterns (Metzler, 1977; Lehninger, 1982; Koolman & Roehm, 2020). However, based on the analysis of experimental diffraction patterns, sometimes opposite conclusions can be drawn. An example of this is the analysis of diffractograms of intermetallic compounds. In 1984, Shechtman et al., Analyzing these diffractograms, came to the conclusion that the structure of intermetallic compounds does not have translational symmetry, so they were called quasicrystals (Shechtman, et al., 1984). However, later, based on the analysis of the same diffraction patterns, it was concluded that the structure of intermetallic compounds has translational symmetry, but in a space of higher dimension (Zhizhin, 2013 a, b, 2014). Pauling proposed to explain the features of the diffractograms of intermetallic compounds by twinning of the icosahedron (Pauling, 1987). However, it was later shown that the unit cell of the structure of intermetallic compounds is a polytope of the highest dimension (Zhizhin, 2013 a, b, 2014). Analysis of Pauling's works on the structure of protein molecules (Pauling & Corey, 1950; Pauling, et al., 1951; Pauling & Corey, 1953; Corey & Pauling, 1953) shows that Pauling's model is nothing more than an assumption. Consider three amino acid residues linked by a peptide bond (Figure 1).

Figure 1.

Spatial image of three amino acid residues linked by a peptide bond

IJARPHM.290380.f01

Complete Article List

Search this Journal:
Reset
Volume 9: 1 Issue (2024)
Volume 8: 1 Issue (2023)
Volume 7: 2 Issues (2022): 1 Released, 1 Forthcoming
Volume 6: 2 Issues (2021)
Volume 5: 2 Issues (2020)
Volume 4: 2 Issues (2019)
View Complete Journal Contents Listing