On the turning away

Abstract : The functional properties of a protein depend mainly on its three-dimensional (3D) structure. They are classically assigned, visualized and analysed through the prism of classical secondary structures composed of repetitive parts (α-helices for 1/3rd of the residues and β-strands for 1/5th, resp.) connected by coil. Two other repetitive structures also exist, namely the PolyProline II and the β-turns. The β-turns have been characterized by a hydrogen bond between N-H and C=O of residues i and i+3 by Venkatachalam [1]. He also characterized the first β-turn types. Later novel turns were defined, some being discarded, leading to a final collection of type I, I’, II, II’, IV, VIa1, VIa2, VIb, and VIII β-turns. Types VIa1, VIa2 and VIb are characterized by the presence of a cis-Proline at residue i+2. Turns that do not fit any of the above criteria are classified as type IV [2]. β-turn IV, i.e. the miscellaneous category, represents near 1/3rd of β-turn residues in protein structure, and is the second most frequent β -turn. 25 years have passed since the last proposition of an extension of the classical definition of β-turns. Over all we have known, it seems a good moment to dig them and to see if some new recurrent conformations are not hidden into this miscellaneous type. An automatic clustering approach based on the rules of β-turn type assignment was designed to search for recurrent new turns inside this miscellaneous type. The four most occurring clusters defined the new β-turn types. Surprisingly, these types, named IV1, IV2, IV3 and IV4, represent half of the type IV β-turns, and are more frequent that many established ones. Type IV1, is in the neighbourhood of type II but with very different amino acid composition, while IV2 is close to type VIII with related amino acid content. Types IV3 and IV4 are in the same dihedral angle region than frequent β-turn type I, but with distinct dihedral angle values [3]. [1] Venkatachalam CM (1968) Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 6:1425-1436. [2] Hutchinson EG, Thornton JM (1996) PROMOTIF--a program to identify and analyze structural motifs in proteins. Protein Sci 5:212-220. [3] de Brevern AG (2016) Extension of the classical classification of β-turns. Sci Rep. 2016 Sep 15;6:33191.
Type de document :
Poster
20e congrès du GGMM (groupe de graphisme et modélisation moléculaire), Aug 2017, Reims, France. 2017
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http://www.hal.inserm.fr/inserm-01575727
Contributeur : Alexandre G. De Brevern <>
Soumis le : lundi 21 août 2017 - 15:37:30
Dernière modification le : mercredi 21 février 2018 - 23:18:14

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  • HAL Id : inserm-01575727, version 1

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Alexandre De Brevern. On the turning away. 20e congrès du GGMM (groupe de graphisme et modélisation moléculaire), Aug 2017, Reims, France. 2017. 〈inserm-01575727〉

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