%0 Journal Article
%T The Influence of Flanking Secondary Structures on Amino Acid Content and Typical Lengths of 3/10 Helices
%A Vladislav Victorovich Khrustalev
%A Eugene Victorovich Barkovsky
%A Tatyana Aleksandrovna Khrustaleva
%J International Journal of Proteomics
%D 2014
%I Hindawi Publishing Corporation
%R 10.1155/2014/360230
%X 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¡ªregions situated between any of two major elements of secondary structure (alpha helices and beta strands)¡ªcontaining 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. 1. Introduction Although 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]. Indeed, there are many cases when a 3/10 helix is present in one 3D structure from Protein Data Bank (http://www.pdb.org/) and absent in another 3D structure of the same 100% identical protein. Ligand binding, 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¨CH 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. Because of the short length, 3/10 helices are prone to appearing or disappearing completely due to the formation or destruction of a single hydrogen bond. 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¨C5]. Even one of the newest methods for secondary structure prediction (C8-SCORPION) has an accuracy of 50% for 3/10 helices prediction when a template of 40% or more
%U http://www.hindawi.com/journals/ijpro/2014/360230/