Third type of secondary structure: Noncooperative mobile conformation. Protein Data Bank analysis

doi:10.1016/0006-291X(87)90736-4

Biochemical and Biophysical Research Communications

Volume 146, Issue 3, 14 August 1987, Pages 934-938

https://doi.org/10.1016/0006-291X(87)90736-4 Get rights and content

Abstract

Analysis of 68 proteins from Protein Data Bank disclosed a new widely spread type of the secondary structure that is designated as mobile (M-) conformation. Helical parameters of M-conformation are close to the poly-L-proline II type helix. Its occurrence in globular proteins approximates that of the β-sheet. The angles corresponding to the position of the M-conformation maximum in distribution of amino acid residues on a conformational map are ϕ: −65°, ψ: 140°. Unique features and high occurrence in proteins make it possible to distinguish the M-conformation as an independent third type of the secondary structure in globular proteins, that should be included in the present classification.

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However, it has been shown that the PPII-helices are also found in the regions of protein or polypeptide that lack significant presence or are completely devoid of Pro residues (Adzhubei et al., 2013). Soman and Ramakrishnan in 1983 (Soman and Ramakrishnan, 1983) reported the presence of PPII-helix in bacteriochlorophyll a-protein and they have subsequently been found to occur frequently in other peptide (Makarov et al., 1992) and protein structures (Adzhubei et al., 1987; Stapley and Creamer, 1999). Even the analyses of backbone conformations of individual residues in protein structures deposited in Protein Data Bank (PDB) (Berman et al., 2000) have shown that the PPII and β-strand conformations have comparable occurrences (Adzhubei et al., 1987).
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Third type of secondary structure: Noncooperative mobile conformation. Protein Data Bank analysis

Abstract

J. Mol. Biol

Science

Biophysica (USSR)

Biopolymers

Biophysica (USSR)