Systematic Distortion of Peptide Bond Angeles in Beta Sheets: Evidence for cis-trans Isomerization?

Abstract

With rare exceptions, peptide bonds at non-praline residues in proteins are modeled exclusively in the trans conformation. Energetic considerations suggest, however, that about 1% of peptide bonds should be in the cis conformation. In cases where cis bonds have been observed in proteins, surprisingly little difference is apparent between chain traces fit with either cis or trans peptide bonds. As a result, it is possible that peptide bonds in proteins may exist in both the trans and cis conformations. In these cases, the electron density at a particular peptide bond would be a weighted average of both forms. If a peptide bond adopts the cis conformation only a few percent of the time, it would be impossible to observe these cis bonds by direct inspection of electron density maps. During structure refinement, however, the presence of residual cis density should systematically distort the stereochemistry of the trans peptide bonds used in the refinement. In this note, the magnitude of this effect is estimated through model calculations on peptides in the beta conformation. The distortions in peptide bond angles observed in well refined proteins structures are consistent with these bonds adopting the cis conformation several percent of the time.

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