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Conformation of the LL and LD hairpin bends with internal hydrogen bonds in proteins and peptides

Chandrasekaran, R and Lakshminarayanan, AV and Pandya, UV and Ramachandran, GN (1973) Conformation of the LL and LD hairpin bends with internal hydrogen bonds in proteins and peptides. In: Biochimica et Biophysica Acta (BBA) - Protein Structure, 303 (1). 14 -27.

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The conformation of three linked peptide units having an internal 4 → 1 type of hydrogen bond has been studied in detail, and the low energy conformations are listed. These conformations all lead to the reversal of the chain direction, and may therefore be called as “hairpin bends” or “U-bends”. Since this bend can occur at the end of two chains hydrogen-bonded in the antiparallel β-conformation, it is also known as the “β-bend”. Two types of conformation are possible when the residues at the second and third Cα atoms are both of type L (the LL bend), while only one type is possible for the LD and the DL bend. The LL bend can also accommodate the sequences LG, GL, GG (G = glycine), while the LD bend can accommodate the sequences LG, GD and GG. The conformations for the sequences DD and DL are exact inverses (or mirror images) of those for the sequences LL and LD, respectively, and have dihedral angles (phi2, ψ2), (phi3, ψ3) of the same magnitudes, but of opposite signs as those for the former types, which are listed, along with the characteristics (length, angle and energy) of the hydrogen bonds. A comparison of the theoretical predictions with experimental data (from X-ray diffraction and NMR studies) on proteins and peptides, show reasonably good agreement. However, a systematic trend is observable in the experimental data, slightly deviating from theory, which indicates that some deformations occur in the shapes of the peptide units forming the bend, differing from that of the standard planar peptide unit.

Item Type: Journal Article
Publication: Biochimica et Biophysica Acta (BBA) - Protein Structure
Publisher: Elsevier Science
Additional Information: Copy right of this article belongs to Elsevier Science.
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 18 Jan 2010 10:19
Last Modified: 19 Sep 2010 05:45
URI: http://eprints.iisc.ac.in/id/eprint/23413

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