The Influence of Flanking Secondary Structures on Amino Acid Content and Typical Lengths of 3/10 Helices

Abstract

We used 3D structures of a highly redundant set of bacterial proteins encoded by genes of high, average, and low GC-content. Four types of connecting bridges—regions situated between any of two major elements of secondary structure (alpha helices and beta strands)—containing a pure random coil were compared with connecting bridges containing 3/10 helices. We included discovered trends in the original “VVTAK Connecting Bridges” algorithm, which is able to predict more probable conformation for a given connecting bridge. The highest number of significant differences in amino acid usage was found between 3/10 helices containing bridges connecting two beta strands (they have increased Phe, Tyr, Met, Ile, Leu, Val, and His usages but decreased usages of Asp, Asn, Gly, and Pro) and those without 3/10 helices. The typical (most common) length of 3/10 helices situated between two beta strands and between beta strand and alpha helix is equal to 5 amino acid residues. The preferred length of 3/10 helices situated between alpha helix and beta strand is equal to 3 residues. For 3/10 helices situated between two alpha helices, both lengths (3 and 5 amino acid residues) are typical.

The part of a long beta hairpin from the scrapie form of the human prion protein is reconstructed in the synthetic CC36 protein

“…For the prediction of secondary structure elements, we used our original propensity scales . Those scales are based on the data obtained from the analysis of three‐dimensional structures of proteins with the maximal similarity of their amino acid sequences equal to 25% . So, we can state that the method we used is a kind of purely ab‐initio method and not homology‐based one.…”

“…To build that scale, we analyzed the amino acid content of alpha helices, beta strands, and random coil regions of 542 proteins from bacteria with different average genomic GC‐content. We used the same set of proteins that has already been described in our work on the 3/10 helices properties . There was no bias in that set associated with the design of the previous study.…”

“…We used the same set of proteins that has already been described in our work on the 3/10 helices properties. 27 There was no bias in that set associated with the design of the previous study. The maximal similarity level in each pair of amino acid sequences of those proteins is 25%.…”

Dynamics and deformability of α-, 310- and π-helices

“…A specific analysis of a 3 10 -helix adjoining the α-helix and β-strand has shown that the composition of 3 10 -helices and β-strands is much more conserved among family members of homologous structures than those adjacent to two helices [26]. The preferred length of the 3 10 -helix occurring between an α-helix and β-strand is equal to 3 residues, but extends to 4 residues when located between two α-helices (α-3 10 -α) [28].…”

Evaluation of peptide designing strategy against subunit reassociation in mucin 1: A steered molecular dynamics approach

“…Taking into account the linearity of the reference peptide, we opted to design linear peptides. As a result we designed peptides with beta sheet forming amino acids namely cysteine, isoleucine, phenylalanine, threonine, tryptophan and tyrosine [ 39 , 40 ]. Proline and glycine were avoided to reduce folding of the peptide.…”