Comprehensive analysis of the distinct nano environments characteristics containing the different secondary structure elements: α- helices, β-sheets, and turns

Abstract

Abstract This work is the third part of our initiative to fully describe the internal protein nano environments (NEs) for the three existing types of secondary structure elements (SSE). In our previous work, the NE of both the α-helix and the β-sheet were analysed. The knowledge acquired in this research is important considering that secondary structure element formation is a crucial step in protein folding and an important phase that precedes the final 3D protein structure. In the current paper, STING´s database of physical-chemical and structural descriptors was used to gather the necessary information to characterize the NE of loops, or, as they are often called, turns. Given that approximately 20% of all protein-type residues form turns, research in this field is essential, and analysis of the obtained results will further contribute to our comprehension of how proteins fold. In addition, the results in this paper will contribute to the better training of algorithms that evaluate the degree of overall protein structure quality and, consequently, structure prediction. This is currently very important given we are witnessing a revolution in algorithms employing artificial intelligence for protein structure prediction. Powered by the STING’s database (wide-ranging protein structure information source), statistical testing was used to retrieve a set of descriptors that fully delineate the NE of turns. By collecting such data, it is then possible to list the variances with respect to the NE of α-helices and β-sheets and, by doing so, establish the most relevant NE descriptors (MRND) for each of the three SSEs. The results show that the α-helical and β-sheet Nes, as well as the amino acid residue composition, all behave in a similar fashion as a “key and lock” system. In other words, it is necessary for a set of specific descriptors to assume respective specific values (within the bounds of a very definite value region) to construct the specific secondary structure element NE at a certain protein location. Consequently, there is a set of descriptors that act together that are required to satisfy specific conditions for secondary structure element occurrences. The very same requirement, we found, occurs in the case of turns.