Different Synergy in Amyloids and Biologically Active Forms of Proteins

Abstract

Protein structure is the result of the high synergy of all amino acids present in the protein. This synergy is the result of an overall strategy for adapting a specific protein structure. It is a compromise between two trends: The optimization of non-binding interactions and the directing of the folding process by an external force field, whose source is the water environment. The geometric parameters of the structural form of the polypeptide chain in the form of a local radius of curvature that is dependent on the orientation of adjacent peptide bond planes (result of the respective Phi and Psi rotation) allow for a comparative analysis of protein structures. Certain levels of their geometry are the criteria for comparison. In particular, they can be used to assess the differences between the structural form of biologically active proteins and their amyloid forms. On the other hand, the application of the fuzzy oil drop model allows the assessment of the role of amino acids in the construction of tertiary structure through their participation in the construction of a hydrophobic core. The combination of these two models—the geometric structure of the backbone and the determining of the participation in the construction of the tertiary structure that is applied for the comparative analysis of biologically active and amyloid forms—is presented.

Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy

“…In this way, a band micelle is obtained, which is generated by amyloid proteins. Amyloids represent a structural form with a hydrophobic core in the form of a tape running along the long axis of fibril surrounding it with better or worse matched bands with low hydrophobicity [48][49][50][51][52]. Thus, amyloids are a synergy that is different from the native form, leading to an alternative solution to the impact and presence of a polar aquatic environment.…”

“…The current analysis is to check the degree of universality of this approach including correctly folded proteins. The structure of the hydrophobic core-its degree of compliance with the idealized distribution-is determined using a model called the fuzzy oil drop model [47][48][49][50][51][52][53][54][55][56][57], in which the idealized distribution of hydrophobicity (T) is expressed using a 3D Gaussian distribution, which is spread over the body of the protein (values of the σ-x, α-y and α-z parameters are selected specifically for a given protein). On the other hand, the actual distribution of hydrophobicity (O) is assessed resulting from the distribution of so-called effective atoms (the average position of atoms included in a given amino acid) and intrinsic hydrophobicity, which is constant for a given amino acid.…”

“…The work shows that the structure of the hydrophobic core is the result of general molecular synergy expressed in the organization of the distribution of hydrophobicity which is the share of all components. This synergy is particularly evident in changes known as amyloid transformation [48][49][50][51].…”

Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity

“…The three groups of proteins-antifreeze type III [7], amyloids [16] and lyases (discussed in this paper)-represent common structural characteristics. This is the presence of structural forms with linear propagation of bands of different hydrophobicity level.…”

“…The linear propagation as observed in amyloids lacks a natural "stop" signal and may continue indefinitely, which explains the unrestricted length of amyloids. The detailed discussion focused on amyloids can be found in [16]. This paper can be treated also as supplementary to the discussion of 3D structure of antifreeze proteins, where solenoid is also present [7].…”