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    Biopolymers. 2007 Jul;86(4):288-97.

    Protein recognition motifs: design of peptidomimetics of helix surfaces.

    Che Y, Brooks BR, Marshall GR.

    Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA. chey@nhlbi.nih.gov

    Helices represent one of the most common recognition motifs in proteins. The design of nonpeptidic scaffolds, such as the 3,2',2''-tris-substituted terphenyl, that can imitate the side-chain orientation along one face of an alpha-helix potentially provides an effective means to modulate helix-recognition functions. Here, based on theoretical arguments, we described novel alpha-helix mimetics which are more effective than the terphenyl at constraining the aryl-aryl torsion angles to those associated with structures suitable for mimicking the alpha-helical twist for side-chain orientation and for superimposing the side chains of residues i, i + 3 or i + 4, i + 7 when compared with the alpha-beta side-chain vectors of the regular alpha-helix with an improved root mean square deviation (RMSD) of approximately 0.5 A. In addition, this study suggests that rotamer distributions around the C(alpha)--C(beta) bonds of these helix mimetics are similar to those of alpha-helices, except that these rotamer distributions show an approximately 60 degrees shift compared to those of alpha-helices when the mimetic axis is superimposed upon the helix axis. This change in rotamer orientation complicates mimicry of the helix surface. (c) 2007 Wiley Periodicals, Inc.

    PMID: 17443711 [PubMed - indexed for MEDLINE]

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