Stereochemical studies on cyclic peptides: Detailed energy minimization studies on hydrogen bonded all-trans cyclic pentapeptide backbones |
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Authors: | H A Nagarajaram C Ramakrishnan |
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Institution: | (1) Molecular Biophysics Unit, Indian Institute of Science, 560 012 Bangalore, India |
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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.
This is part XV of the series. Part XIV in this series is Ramakrishnanet al 1987. |
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Keywords: | Cyclic pentapeptide conformational studies reverse turns β -turn γ -turn energy minimization |
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