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Comprehensive analysis of the helix‐X‐helix motif in soluble proteins
Author(s) -
Deville Julie,
Rey Julien,
Chabbert Marie
Publication year - 2008
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21879
Subject(s) - ramachandran plot , dihedral angle , helix (gastropod) , polyproline helix , crystallography , linker , speed wobble , chemistry , screw axis , alpha helix , stereochemistry , protein structure , physics , geometry , biology , mathematics , circular dichroism , peptide , molecule , operating system , ecology , biochemistry , hydrogen bond , organic chemistry , classical mechanics , snail , computer science
α‐Helices are the most common secondary structures found in globular proteins. In this report, we analyze the stereochemical and sequence properties of helix‐X‐helix (HXH) motifs in which two α‐helices are linked by a single residue, in search of characteristic structures and sequence signals. The analysis is carried out on a database of 837 nonredundant HXH motifs. The kinks are characterized by the bend angle between the axes of the N‐terminal and C‐terminal helices and the wobble angle corresponding to the rotation of C‐terminal helix axis on the plane perpendicular to the N‐terminal one. The phi‐psi dihedral angles of the linker residue are clustered in six distinct areas of the Ramachandran plot: two areas are located in the additional allowed α region (α 1 and α 2 ), two areas are in the additional allowed β region (β 1 and β 2 ) and two areas have positive phi values (α L and β M ). Each phi/psi region corresponds to characteristic bend and wobble angles and amino acid distributions. Bend angles can vary from 0° to 160°. Most wobble angles correspond to a counter‐clockwise rotation of the C‐terminal helix. Proline residues are rigorously excluded from the linker position X but have a high propensity at position X+1 of the β 1 and β 2 motifs (12 and 7, respectively) and at position X+3 of the α 1 motifs (9). Glycine linkers are located either in the α L region (20%) or in the β M region (80%). This latter conformation is characterized by a marked bend angle (124° ± 18°) and a clockwise wobble. Among other amino acids, Asn is remarkable for its high propensity (>3) at the linker position of the α 2 , β 1 , and β 2 motifs. Stabilization of HXH motifs by H‐bonds between polar side chains of the linker and polar groups of the backbone is determined. A method based on position‐specific scoring matrices is developed for conformational prediction. The accuracy of the predictions reaches 80% when the method is applied to proline‐induced kinks or to kinks with bend angles in the 50°–100° range. Proteins 2008. © 2008 Wiley‐Liss, Inc.