Glutamine, hydrogen-bonding

The new crystal structure of the ribosome—RFl complex sheds more light into the interactions between the GGQ motif and the peptidyltransferase center. This complex represents the product state of peptide release since a deacylated tRNA is bound to the P site. Importantly, the main chain amide of the conserved glutamine hydrogen bonds to the 3 OH of A76 in the P site, which is the leaving group of the hydrolysis... 

As a p hydroxy derivative of phenylalanine tyrosine has properties similar to those of phenylalanine plus the ability to engage m hydrogen bonding via its —OH group Asparagine and glutamine are not amines they are amides The side chains of both O... 

Fig. 4. Ramachandran plots of glutamines (A) making side chain-to-backbone hydrogen bonds with the next residue in sequence (B). Filled circles denote residues where the glutamine is in the PPII conformation. Open circles denote all residues where the glutamine is not in the PPII conformation.

Glutamine can also be considered an outlier if it forms a side chain-to-backbone hydrogen bond as hypothesized by Stapley and Creamer... 

Fig. 6. Ramachandran plots for simulated Ac-Ala-Xaa-Ala-Ala-NMe peptides with Xaa = glutamine or asparagine, with a constrained side chain-to-backbone hydrogen bond. Conformational distribution for glutamine i (A) and for the residue i +1 to which the glutamine is hydrogen-bonded (B). Conformational distribution for asparagine i (C) and for the residue i +1 to which it is hydrogen-bonded (D).

B) Surface and stick representation of the model, viewed down the fibril axis. (The top coil is shown as sticks, with the remainder showing van derWaals radii.) The glutamine side chains are proposed to form hydrogen-bonded stacks parallel to the fibril axis. The large diameter of the cylinder results in a pore down the center. Both panels were generated with Pymol (DeLano, 2002). 

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