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Construction and conformational behavior of peptoids with cis-amide bond geometry: design of a peptoid with alternate φ, ψ values of inverse PP-II/PP-II and PP-I structures

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Abstract

In peptoids due to the absence of amide protons, the backbone is devoid of hydrogen bond donor, linked by tertiary amide, which can be iso-energetic between cis and trans-amide bond geometry. The peptoids can be realized with cis amide bond if the side chain of ith residue can engage the carbonyl group of ith-1 residue in CH--O interactions. Simulations studies both in water and DMSO have been carried out. The peptoid Ac-(Ntle)7 -NMe2 can adopt degenerate conformations with alternate φ, ψ values of inverse PP-I and PP-I type structure’s, or vice versa in water. In DMSO, Ac-(Ntle)7-NMe2 also adopts inverse PP-I type structure. Like polyproline, molecule adopting a rigid structure can be used as molecular markers or spacers in biological studies.

The peptoid Ac-(Nala-Ntle)3-NMe2 with alternate trans and cis amide bond geometry for Nala and Ntle residue corresponding to inverse PP-II/PP-II type and for Ntle residue of PP-I type.

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Acknowledgments

We acknowledge Department of Biotechnology, India for financial support.

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Authors and Affiliations

  1. Department of Biophysics, Panjab University, Chandigarh, 160014, India

    Fateh Singh Nandel, Radhika Rani Jaswal, Avneet Saini, Vibhuti Nandel & Mohd Shafique

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  1. Fateh Singh Nandel
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  2. Radhika Rani Jaswal
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  3. Avneet Saini
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Correspondence to Fateh Singh Nandel.

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Nandel, F.S., Jaswal, R.R., Saini, A. et al. Construction and conformational behavior of peptoids with cis-amide bond geometry: design of a peptoid with alternate φ, ψ values of inverse PP-II/PP-II and PP-I structures. J Mol Model 20, 2429 (2014). https://doi.org/10.1007/s00894-014-2429-8

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