Spatial models of the β - structures of protein molecules, forming layers of amino acids, in principle, of unlimited length for different conformations 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. A model that simultaneously contains β - structures in parallel and anti - parallel positions and α - spirals. The turn of the polypeptide chain, which is often found in globular proteins, has been studied in higher dimensional space.
TopIntroduction
At present, in numerous works of the author (Zhizhin, 2016, 2018, 2019 c, 2021 a, b, c), the highest dimension of biomolecules, including sugar molecules, phosphoric acid residue and nucleic acids, has been shown. The established ideas about the genetic code are based on the assumption that biomolecules are three-dimensional (Gamov, Rich, Yeas, 1956; Yeas, 1969; Crich, 1966) which contradicts the real geometry of biomolecules. Currently, the accepted genetic code is that each amino acid residue is encoded by three nucleotides in nucleic acids. It is believed that this is the only way to match nucleotides and amino acid residues due to the different number of types of nucleotides and types of amino acid residues. A list of this correspondence has been proposed (see, for example, Spirin, 2019), which is considered the universal genetic code for all living organisms. However, experimental studies in recent years (Spirin, 2019) have discovered many deviations from the proposed genetic code in animals, protozoa, bacteria and fungi, algae, and plants. It is expected that new examples of deviations from the universal genetic code will be discovered in the future. Many amino acid residues are degenerate (corresponding to several triplets); for some amino acid residues this degeneracy reaches significant values. Therefore, ideas about the genetic code must be corrected in connection with the latest studies of the geometry of biomolecules. This chapter is dedicated to this. The first part of the chapter deals with the established ideas about the genetic code with critical remarks about its justification. The second part of the chapter presents a new concept of the genetic code, which takes into account the higher dimension of biomolecules, takes into account the geometric properties and features of polytopes of higher dimension (Zhizhin, 2019). This concept requires further research and experimental confirmation.