4.1. Dataset of 3β-Corner Structures

In this study, we focused on a simple type of SSS—3β-corner. The aim of this study was to analyze the stability of 3β-corner as an autonomous unit or outside the protein globule in an aqueous environment. A set of 330 structures of the 3β-corner type was selected from the Protein Data Bank (PDB) (https://www.rcsb.org/, accessed on 5 August 2022) to perform MD experiments with the following analysis of standard deviation, change in gyration radius, solvent-accessible area, lifetime of the major conformer and torsion angles, and the number of hydrogen bonds reported to characterize the stability of proteins. Super-secondary 3β-corner structures are widely distributed, and there are a few small proteins consisting of only the 3β-corner and short irregular regions in nature [15,16].

The collected dataset was organized from β-proteins, most of which contained small β-barrels according to the SCOP [17] classification (https://scop.berkeley.edu/, accessed on 5 August 2022) folds b.34 (SH3-like; 21 superfamilies), b.43 (common domain of reductase/isomerase/elongation factor; three superfamilies), b.47 (trypsin-like serine proteases; one superfamily), b.55 (domain-like PH; one superfamily), etc. (see Table S6) [17,18,19]. Small stacks of β-barrel represent a closed structure, wherein the first and last β-weights were stabilized by hydrogen bonds [20]. The β-barrel structures can also be represented as two orthogonally arranged β-sheets [21]. Such β-barrel structures are characterized by a few β-strands (n = 3–5) and an elliptical type of cross-section with high shear values (S~6–10), which provide a tight fit—a “flattened” ellipse. The 3β-corner structural motifs ordered as “β-Strand → Coil → β-Strand → Coil → β-Strand” were extracted from the β-barrel folds. The correlation of amino acid residues within the selected structures to elements of the secondary structure was elaborated by using three STRIDE algorithms [22], DSSP [23], and iCn3D [24]. The results of convergence between three algorithms utilized for the identification of elements of the secondary structure are presented in Table S7. The match rate between STRIDE/DSSP, Stride/iCn3D, and DSSP/iCn3D was approximately 50% (Table S7). β-Strands in the 3β-corner structure are usually short and consist of 4–6 to 10 amino acid residues, connected by loops. Short loops (from three to seven amino acid residues) shape a turn, while long loops (8–12 amino acid residues) are characterized by an unstructured shape. The studied dataset was represented by motifs extracted from proteins of various origins and containing different lengths of its constituent elements (Figure 7 and Table S4).

Origin of proteins in which 3β-corners were identified (a); length distribution of 3β-corners in the examined dataset (b).

SSSs were selected for homologous and non-homologous proteins of various origins (Figure 7a). Most of these proteins belong to humans, animals, and bacteria. There are also small groups of plant and viral proteins (Figure 7a). This observation is consistent with the variety of annotated protein structures in the PDB for different entities.

The analysis of lengths amongst selected 3β-corners showed that the majority of studied structures were 25–40 amino acids in length. Moreover, depending on the length, the maximum distribution of 3β-corners fell on 30–35 amino acid residues (Figure 7b), and only a few of the 3β-corners consisted of 45–55 amino acid residues.

The gathered 3β-corners were extracted from the PDB and SCOP and are presented in Table S6.