Converting cis peptides into trans configuration. WARNING: The cispeptide plugin identifies all cis peptide bonds. As noted in the introduction, there are cases in which cis peptides do occur in proteins. Thus, it should be checked if a given cis peptide is real or is a mistake. This can be done by literature research, by comparing high resolution crystallographic models, or by comparing ...

1999年11月19日 · In proteins, the partial double bond character of the peptide bond results in two conformations depending on the value of the dihedral angle, ω [C α (1)-C(1)-N(1′)-C α (1′)]: cis and trans (with ω = 0 and 180°, respectively) Pauling 1960, Ramachandran and Sasisekharan 1968 (Figure 1(a)). The isomer with the two C α atoms trans to each other is favoured overwhelmingly due to the ...

2023年11月21日 · Cis-peptide bonds are rare in proteins, and building blocks less favorable to the trans-conformer have been considered destabilizing. Although proline tolerates the cis-conformer modestly among ...

Abstract: This paper focuses on cis-/trans-conformational interchanges of amide bonds in cyclic peptides that contain N-unsubstituted amino acids, N-methylated amino acids, and prolines.Conformational preferences of such cyclic peptides and their analogs are discussed. Proline has strong influences on the conformation due to the five-membered cyclic structure.

2012年1月8日 · The presence of energetically less favourable cis peptides in protein structures has been observed to be strongly associated with its structural integrity and function. Inter-conversion between the cis and trans conformations also has an important role in the folding process. In this study, we analyse the extent of conservation of cis peptides among similar folds. We look at both the amino ...

Checking the peptide configuration. In order to determine the configuration of each peptide bond (cis/trans), the dihedral angle O-C-N-CA is calculated. If the absolute value is above a predefined cut-off (85 degrees), the peptide bond is considered to be in the cis configuration. Conversion of peptide configuration from cis to trans

Commonly, the fraction of cis isomer of nonprolyl peptide bonds is considered to be negligible in accordance with literature values of ∼ 0.15% for the fraction of cis isomer per peptide bond 20.

1999年11月19日 · A comparison of cis peptides containing proline and non-proline residues show differences in conformation, location in the secondary structure and in relation to the centre of the molecule, and relative accessibilities of residues. Relevance of the results in mutation studies and the cis-trans isomerization during protein folding is discussed.

1999年2月12日 · In a non-redundant set of 571 proteins from the Brookhaven Protein Data Base, a total of 43 non-proline cis peptide bonds were identified. Average geometrical parameters of the well-defined cis peptide bonds in proteins determined at high resolution show that some parameters, most notably the bond angle at the amide bond nitrogen, deviate significantly from the corresponding one in the trans ...

2018年12月1日 · Multidimensional magic-angle spinning solid-state NMR experiments are described that permit cis and trans peptide bonds in uniformly 13 C, 15 N-labeled peptides and proteins to be unambiguously distinguished in residue-specific manner by determining the relative orientations of the amide 13 C′ CSA and 1 H-15 N dipolar coupling tensors. The experiments are demonstrated for model peptides ...