Ω‐Turn: A novel β‐turn mimic in globular proteins stabilized by main‐chain to side‐chain CH···O interaction. Issue 2 (28th November 2014)

• Record Type: Journal Article
• Authors: Dhar, Jesmita; Chakrabarti, Pinak; Saini, Harpreet; Raghava, Gajendra Pal Singh; Kishore, Raghuvansh
• Is Part Of: Proteins. Volume 83:Issue 2(2015)
• Page Start: 203
• Page End: 214
• Publication Date: 2014-11-28
• Subjects: Proteins -- Periodicals; Proteins -- Periodicals; 572.6
• DOI: 10.1002/prot.24720
• Languages: English
• ISSNs: 0887-3585

Abstract

<abstract abstract-type="main"> <title>ABSTRACT</title> <p>Mimicry of structural motifs is a common feature in proteins. The 10‐membered hydrogen‐bonded ring involving the main‐chain CO in a β‐turn can be formed using a side‐chain carbonyl group leading to Asx‐turn. We show that the NH component of hydrogen bond can be replaced by a C<sup>γ</sup>‐H group in the side chain, culminating in a nonconventional CH···O interaction. Because of its shape this β‐turn mimic is designated as ω‐turn, which is found to occur ∼three times per 100 residues. Three residues (<italic>i</italic> to <italic>i</italic> + 2) constitute the turn with the CH···O interaction occurring between the terminal residues, constraining the torsion angles <italic>ϕ<sub>i</sub></italic><sub> + 1</sub>, <italic>ψ<sub>i</sub></italic><sub> + 1</sub>, <italic>ϕ<sub>i</sub></italic><sub> + 2</sub> and <italic>χ</italic>′<sub>1(</sub><italic><sub>i</sub></italic><sub> + 2)</sub> (using the interacting C<sup>γ</sup> atom). Based on these angles there are two types of ω‐turns, each of which can be further divided into two groups. C<sup>β</sup>‐branched side‐chains, and Met and Gln have high propensities to occur at <italic>i</italic> + 2; for the last two residues the carbonyl oxygen may participate in an additional interaction involving the S and amino group, respectively. With Cys occupying the <italic>i</italic> + 1 position, such turns are found in the metal‐binding sites. N‐linked glycosylation occurs at the consensus pattern Asn‐Xaa‐Ser/Thr; with Thr at <italic>i</italic> + 2, the sequence can adopt the secondary structure of a ω‐turn, which may be the recognition site for protein modification. Location between two β‐strands is the most common occurrence in protein tertiary structure, and being generally exposed ω‐turn may constitute the antigenic determinant site. It is a stable scaffold and may be used in protein engineering and peptide design. Proteins 2015; 83:203–214. © 2014 Wiley Periodicals, Inc.</p> </abstract>