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J Chem Theory Comput. 2013 Jan 8;9(1):650-657. Epub 2012 Nov 5.

Exploring the Energy Landscapes of Cyclic Tetrapeptides with Discrete Path Sampling.

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  • 1School of Chemistry, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K.

Abstract

Cyclic tetrapeptides are an important class of biologically active molecules that exhibit interesting conformational dynamics, with slow interconversion of several different structures. We present calculations on their energy landscapes using discrete path sampling. In acyclic peptides and large cyclic peptides, isomers containing cis-peptide groups are much less stable than the all-trans isomers and separated from them by large barriers. Strain in small cyclic peptides causes the cis and trans isomers to be closer in energy and separated by much lower barriers. If d-amino acids or proline residues are introduced, isomers containing cis-peptides become more stable than the all-trans structures. We also show that changing the polarity of the solvent has a significant effect on the energy landscapes of cyclic tetrapeptides, causing changes in the orientations of the peptide groups and in the degree of intramolecular hydrogen bonding.

PMID:
23596359
PMCID:
PMC3624815
DOI:
10.1021/ct3005084
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