The Relationship between Hierarchical Chiral Structures of Proteins and their Functions
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CULAR BIOPHYSICS
The Relationship between Hierarchical Chiral Structures of Proteins and Their Functions E. V. Malyshkoa, *, O. E. Bagrovaa, and V. A. Tverdislova aDepartment
of Physics, Moscow State University, Moscow, 119991 Russia *e-mail: [email protected]
Received December 28, 2019; revised December 28, 2019; accepted February 10, 2020
Abstract— The specific characteristics of the distribution of secondary structures and coiled-coil superhelix structures were investigated for the first time, while taking the sign of chirality into account, in polypeptide chains of proteins belonging to eight functional classes: viral proteins, chaperones, oxidoreductases, hydrolases, structural proteins, proteins involved in exocytosis and endocytosis, and electron-transport proteins. The patterns of protein structure that are common for all studied classes and those typical for each class are described. Keywords: chirality, proteins, secondary structure, α-helix, β-sheet, superhelix DOI: 10.1134/S0006350920030148
For decades, investigation of physical principles underlying the formation of unique structures of biological macromolecules and the mechanisms of their functioning has been a topical issue of molecular biophysics. However, the fundamental questions that concern the mechanisms of intra- and supramolecular structure formation, as well as the functioning of macromolecules as molecular machines, still remain largely unanswered. This work was aimed at identifying patterns in the distribution of secondary structures that form the dynamic backbone of protein molecules. Research on patterns and relationships between the chiral protein structure and its functions could provide deeper insights into the fine mechanisms of conformational changes that occur in proteins globules during their functioning, in particular, by analyzing the structure of their polypeptide chains. This study is based on the analysis of the chirality sign of the structures. In our opinion, the phenomenon of chirality plays a key role in protein folding. The first studies that attempted to predict the secondary structure of proteins based on their known primary sequence date back to the second half of the 20th century. As an example, in the 1970s, Chou and Fasman proposed a method of secondary structure prediction that had an accuracy of 50 to 60% [1]. The presence of secondary structures in proteins was analyzed in a seminal study by Adzhubei et al. [2]. However, early research did not describe the distribution of structures along the protein chain, but only their general abundance in the protein. Furthermore, the sign of the secondary structure chirality was not accounted
for as well. A.A. Zamyatnin noted that many oligopeptide molecules of equal length perform identical functions [3]. It is possible that on higher levels of protein structure organization, chirality patterns might be more clearly associated with protein function. Previously, we proposed and substantiated a hypothesis on the regularity of chirality relationships in intra- and sup
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