Although the overall primary sequence identity is modest (37%), the aligned predicted secondary structure of the two proteins in placement of helical and sheet segments is in 92% agreement.
Our results suggest that the resulting amphiphilic peptides can, despite lacking the essential β-sheet segment, effectively associate under physiological conditions into supramolecular immunofibers (IFs) while preserving their native α-helical conformation.
The peptide sequence analysed originates from a previously reported study, which identified potent inhibitors of human leukocyte elastase from screening a combinatorial peptide library based on the short protein β-sheet segment that forms the reactive site loop of Bowman-Birk inhibitors.
Interestingly, all AprB models of the SOB Apr lineage I possessed in the antiparallel beta-sheet segment an elongated loop by amino acid insertion between the secondary structure element 8 and 9 that comprised predominantly negatively charged residues (see Fig. 4 panels C and E; supplementary data material Table S1 and Figure S1, compare panels E/F).
The PASTA energy for the antiparallel β-sheet segment for S-MB is −6.07, significantly lower than that of the most likely pairing of the C-terminal domain of S-MB (i.e., segment 34 40) with a relative energy of −5.49.
Subfamily CIII is very similar to CII, except that all members of the CIII subfamily exhibit one intron in the ACD and another in the third β-sheet segment.
Here, we focus on systematic substitutions of valine residues present in β-sheet segments of a β-helical building block excised from Escherichia coli galactoside acetyltransferase, residues 131 165.
The recurrence of the β-bend suggests a general mode of connecting long parallel β-sheet segments that would allow the growth of partially ordered fibril structures.
Our new model can be described as a super-helical arrangement of flat β-sheet segments linked by planar turns or bends.
The identification of a coherent organization beyond that of the β-sheet segments in different folds rich in parallel β-sheets suggests a higher degree of ordered structure in protein fibrils, in agreement with their low solubility and dense molecular packing.
The DSSP plot (Figure 11) indicates that the peptide assumes a stable secondary structure with well defined loop and β-sheet segments.
