• Stereochemical studies on cyclic peptides: Detailed energy minimization studies on hydrogen bonded all-trans cyclic pentapeptide backbones

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      https://www.ias.ac.in/article/fulltext/jbsc/020/05/0591-0611

    • Keywords

       

      Cyclic pentapeptide; conformational studies; reverse turns; β-turn; γ-turn; energy minimization

    • Abstract

       

      Conformational studies have been carried out on hydrogenbonded all-trans cyclic pentapeptide backbone. Application of a combination of grid search and energy minimization on this system has resulted in obtaining 23 minimum energy conformations, which are characterized by unique patterns of hydrogen bonding comprising of β- and γ-turns. A study of the minimum energy conformationsvis-a-vis non-planar deviation of the peptide units reveals that non-planarity is an inherent feature in many cases. A study on conformational clustering of minimum energy conformations shows that the minimum energy conformations fall into 6 distinct conformational families. Preliminary comparison with available X-ray structures of cyclic pentapeptide indicates that only some of the minimum energy conformations have formed crystal structures. The set of minimum energy conformations worked out in the present study can form a consolidated database of prototypes for hydrogen bonded backbone and be useful for modelling cyclic pentapeptides both synthetic and bioactive in nature.

    • Author Affiliations

       

      H A Nagarajaram1 C Ramakrishnan1

      1. Molecular Biophysics Unit, Indian Institute of Science, Bangalore - 560 012, India
    • Dates

       
  • Journal of Biosciences | News

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