Article (Scientific journals)
Pex, Analytical Tools For Pdb Files. II. H-Pex: Noncanonical H-Bonds In Alpha-Helices
Thomas, Annick; Benhabiles, N.; Meurisse, R. et al.
2001In Proteins, 43 (1), p. 37-44
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Abstract :
[en] We use the H-Pex (Thomas et al., this issue) to analyze the main chain interactions in 131 proteins. In antiparallel beta-sheets, the geometry of the N...O bond is: median N...O distances, 2.9 SA, C==O...N angles at 154 degrees and the C alpha--C==O...H angles are dispersed around 3 degrees. In some instances, the other side of the C==O axis is occupied by a HC alpha. As recently supported by Vargas et al. (J Am Chem Soc 2000;122:4750-4755) C alpha H...O and NH...O could cooperate to sheet stability. In alpha-helices, the main chain C==O interact with the NH of their n + 4 neighbor on one side, and with a C beta H or C gamma H on the other side. The median O...N distance (3.0 A) and C==N angle (147 degrees) suggest a canonical H-bond, but the C alpha--C==O...H dihedral angle invalidates this option, since the hydrogen attacks the oxygen at 122 degrees, i.e., between the sp(2) and pi orbitals. This supports that the H-bond is noncanonical. In many instances, the C gamma H or the C beta H of the n + 4 residue stands opposite to the NH with respect to the oxygen. Therefore, we propose that, in alpha-helices, the C gamma H or C beta H and the NH of the n + 4 residue hold the oxygen like an electrostatic pincher.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Thomas, Annick ;  Université de Liège - ULiège > Chimie et bio-industries > Centre de Bio. Fond. - Section de Biologie moléc. et numér.
Benhabiles, N.
Meurisse, R.
Ngwabije, R.
Brasseur, Robert ;  Université de Liège - ULiège > Gembloux Agro-Bio Tech
Language :
English
Title :
Pex, Analytical Tools For Pdb Files. II. H-Pex: Noncanonical H-Bonds In Alpha-Helices
Publication date :
2001
Journal title :
Proteins
ISSN :
0887-3585
eISSN :
1097-0134
Publisher :
Wiley-Liss Inc, United States - New York
Volume :
43
Issue :
1
Pages :
37-44
37-44
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 25 June 2010

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