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Side-chain flips

Figure 13.1 Correction of a structure by side-chain flipping. The original structure after CNS refinement is shown in (a) and after the recommended correction of WHATCHECK in (b). Carbon atoms are grey, oxygens white, and nitrogens black. Asn 144 and Glu 145 are the labelled adjacent residues in a helix, shown as a ribbon. After a 180 degree rotation about the chi-2 dihedral of Asn 144, the side chain amide nitrogen is now in position to hydrogen bond, shown as the labelled dashed line, to the carboxylate of Glu 145. Image rendered by ribbons. Figure 13.1 Correction of a structure by side-chain flipping. The original structure after CNS refinement is shown in (a) and after the recommended correction of WHATCHECK in (b). Carbon atoms are grey, oxygens white, and nitrogens black. Asn 144 and Glu 145 are the labelled adjacent residues in a helix, shown as a ribbon. After a 180 degree rotation about the chi-2 dihedral of Asn 144, the side chain amide nitrogen is now in position to hydrogen bond, shown as the labelled dashed line, to the carboxylate of Glu 145. Image rendered by ribbons.
Fig. 13 DNA-protein CT reactions. The DNA-bound protein, methyltransferase Hhal (mutant Q237W), flips a base out of the DNA double helix and inserts a trytophan side chain leaving the /r-stack largely unperturbed. This intercalated trytophan moiety transfers an electron to [Ru(bpy )(dppz)(phen)]3+, generated by flash quench, over 50 A away. Adapted from [164]... [Pg.109]

Fig. 5. Types of motion in proteins detected by nmr. Rotation about methyl groups is easily detected from threefold symmetry and is rapid. Rotation or flipping about the C(J—Cy bonds of tyrosine or phenylalanine has been observed readily (see text) because of the twofold symmetry of the aromatic ring. Rotation of more complex side chains is more difficult to define because of the lack of symmetry. Fig. 5. Types of motion in proteins detected by nmr. Rotation about methyl groups is easily detected from threefold symmetry and is rapid. Rotation or flipping about the C(J—Cy bonds of tyrosine or phenylalanine has been observed readily (see text) because of the twofold symmetry of the aromatic ring. Rotation of more complex side chains is more difficult to define because of the lack of symmetry.
A further modification of the active-center model was based on the consideration that the vacancy in the active center is strongly shielded by the polymer chain, mainly by the CH2 and CH3 groups of the second monomer unit. As a result, the vacant site is blocked and inaccessible for olefin coordination. Kissin et al. suggest a polymerization center with two vacancies one shielded and the other open for complexation.344,345 After each insertion step the end of the growing polymer chain flips from side to side and the two vacant sites are alternately available for alkene coordination. [Pg.762]

The Photoactive Yellow Protein (PYP) is thought to be the photoreceptor responsible for the negative phototaxis of the bacterium Halorhodospira halophila [1]. Its chromophore, the deprotonated 4-hydroxycinnamic (or p-coumaric) acid, is covalently linked to the side chain of the Cys69 residue by a thioester bond. Trans-cis photoisomerization of the chromophore was proved to occur during the early steps of the PYP photocycle. Nevertheless, the reaction pathway leading to the cis isomer is still discussed (for a review, see ref. [2]). Time-resolved spectroscopy showed that it involves subpicosecond and picosecond components [3-7], some of which could correspond to a flipping motion of the chromophore carbonyl group [8,9]. [Pg.421]


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