In peptides and proteins, adjacent amino acids are linked together via a peptide bond. In the majority of the cases the peptide bond is found to be in trans conformation in the majority of the cases. Only a small fraction of peptide bonds in proteins is reported to be in cis conformation. Most of these instances (>90%) occur when the peptide bond is an imide (X-Pro) rather than an amide bond (X-nonPro). Due to the implication of cis/trans isomerization in many biologically significant processes, the accurate prediction of the peptide bond conformation is of high interest.

The two energetically preferred conformations of the peptide bond, cis and trans, depend on the value of the dihedral angle ω [Ca(i) – C(i) – N(i+1) – Ca(i+1)], with ω=0° and 180°, respectively (Figure 1).

Figure 1: Representation of the cis and trans conformational isomers of a Phenylalanine-Proline peptide bonds. In the cis conformation the two Ca atoms are locked on the same side of the peptide bond, whereas in the trans configuration the Ca atoms lie on opposite sides of the double bond.

It should be noted that the Ca(i) – Ca(i+1) distance in cis conformation is nearly 1A shorter than in the trans conformation and thus, there is strong correlation between the resolution of the protein structure and the cis conformation content. The cis conformation occurs rarely in polypeptides because of the higher intrinsic energy compared to the trans conformation. However, in the case of X-Pro amino acid pairs the situation is slightly different, due to the smaller energy difference between cis and trans isomer.

Cis peptide bonds are very important in a variety of biological processes. Cis prolyl residues are more often conserved than the surrounding amino acids, which show the same extent of conservation as the whole protein, pointing out the significance of cis peptide bonds in protein structure and function during evolution. In addition, cis peptide bonds, especially the ones between non-proline residues, are located near the active sites of proteins or have roles in the function of the protein molecule. Several cis peptide bonds play a vital role in the final structure and function, as well as the folding and stability of many proteins. Moreover cis prolyl residues were also shown to be an important step in regulation, cell signaling and splicing of the protein molecules. The occurrence of cis amide peptide bonds has been associated with steric strain in proteins and it has been speculated that these sites of strain comprise some kind of energy reservoir for the protein. The functional relevance of the proline cis/trans equilibrium is supported by the existence of special enzymes called peptidyl prolyl isomerases (PPIases) which catalyze the cis/trans isomerization of the X-Pro bond and are also implicated in the induction of severe diseases such as cancer, AIDS, Alzheimer’s disease and other neurodegenerative disorders. Hence, accurate discrimination between the cis/trans conformations, will greatly contribute towards reliable prediction of protein structure and function.

For the past few years, the Unit of Medical Technology and Intelligent Information Systems, has been studying the conformational isomers of the peptide bond using state-of-art data mining techniques and has developed several new algorithms, for the exploration of the peptide bond isomerization. An SVM based method has been developed for the accurate prediction of both proline and non-proline cis/trans isomerization [1, 2]. Moreover, pattern based approaches, enriched with literature information, have revealed several important aspects regarding the nature as well as the interactions of proline and non-proline cis peptide bonds [3, 4, 5]. Ongoing work, supported by previous findings, suggests that cis peptide bonds are often found at or near active sites of proteins or regions highly associated with the function of the protein molecule.