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

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.

SUBMITTER: Oakley MT

PROVIDER: S-EPMC3624815 | biostudies-other | 2013 Jan

REPOSITORIES: biostudies-other

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

Oakley Mark T MT Johnston Roy L RL

Journal of chemical theory and computation 20121105 1

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 ...[more]

PMID: 23596359

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