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Conformational and Sequence Signatures in $\beta$ Helix Proteins

Iengar, Prathima and Joshi, NV and Balaram, Padmanabhan (2006) Conformational and Sequence Signatures in $\beta$ Helix Proteins. In: Structure, 14 (3). pp. 529-542.

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Abstract

$\beta$ helix proteins are characterized by a repetitive fold, in which the repeating unit is a $\beta$-helical coil formed by three strand segments linked by three loop segments. Using a data set of left- and right-handed $\beta$helix proteins, we have examined conformational features at equivalent positions in successive coils. This has provided insights into the conformational rules that the proteins employ to fold into $\beta$helices. Left-handed $\beta$ helices attain their equilateral prism fold by incorporating corners with the conformational sequence $P_I_I-P_I_I-{\alpha}_L-P_I_I$, which imposes sequence restrictions, resulting in the first and third PII residues often being G and a small, uncharged residue (V, A, S, T, C), respectively. Right-handed $\beta$ helices feature mid-sized loops (4, 5, or 6 residues) of conserved conformation, but not of conserved sequence; they also display an $\alpha$-helical residue at the C-terminal end of L2 loops. Backbone conformational parameters $(\phi,\Psi)$ that permit the formation of continuous, loopless $\beta$ helices (Perutz nanotubes) have also been investigated.

Item Type: Journal Article
Additional Information: This Copyright belongs to Elsevier.
Keywords: Proteins
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Division of Biological Sciences > Centre for Ecological Sciences
Date Deposited: 25 Aug 2008
Last Modified: 19 Sep 2010 04:25
URI: http://eprints.iisc.ernet.in/id/eprint/6285

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