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.
Highlights
3/10 helices play important roles in the folding of proteins, historically they were thought to be unstable and relatively rare [1, 2]
The main issue focused on by this study is the nature of 3/10 helices. Are they nothing but random coil with two occasionally overlapping instable “i–i + 3” “main chainmain chain” hydrogen bonds, or are they short alpha helices with different pattern of hydrogen bonding? there are two answers to that question. 3/10 helices composed of 3 amino acids can be thought of as products of a random coil, while 3/10 helices composed of 5 amino acids demonstrate many similarities to the N-termini of alpha helices
We found that 3/10 helices situated between two beta strands have more features distinguishing them from the random coil than 3/10 helices situated between other major secondary structure elements
Summary
3/10 helices play important roles in the folding of proteins (as parts of transmembrane helices, as interactive interfaces, as immunogenic epitopes, and as fragments of active centers), historically they were thought to be unstable and relatively rare [1, 2]. Changes in pH, interactions with other proteins, and other specific conditions may influence distances between nitrogen and oxygen atoms from the protein backbone and angles between N–H and C=O groups. Some of those changes lead to the appearance or disappearance of certain hydrogen bonds, frequently making N- and C-termini of beta strands and alpha helices longer or shorter. Even relatively small changes in distances between atoms may lead to transitions from alpha helix to 3/10 helix and vice versa Those structural transitions are well studied in relatively short model peptides [3,4,5]. The authors of the “C8-SCORPION” state that such accuracy (50%) is a good result for 3/10 helices prediction [6]
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