ArticleJournal of chemical theory and computation2013
Exploring the Energy Landscapes of Cyclic Tetrapeptides with Discrete Path Sampling.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Pharmacological potential of the marine peptide cyclo(L-phenylalanyl-L-prolyl) against both multidrug-resistant, gram-negative Acinetobacter baumannii and gram-positive Staphylococcus aureus: structure - activity relationship, computational and experimental studies.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.The journal of physical chemistry. B · 2022Article
- Crossing of the Cystic Barriers ofMolecules (Basel, Switzerland) · 2021Article
- Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides.The journal of physical chemistry. B · 2021Article
- Synthesis of cyclotetrapeptide analogues of c-PLAI and evaluation of their antimicrobial properties.Royal Society open science · 2021Article
- Bioinformatics and Biosimulations as Toolbox for Peptides and Peptidomimetics Design: Where Are We?Frontiers in molecular biosciences · 2020Review
- Designing Well-Structured Cyclic Pentapeptides Based on Sequence-Structure Relationships.The journal of physical chemistry. B · 2018Article
- The reactivity and conformational control of cyclic tetrapeptides derived from aziridine-containing amino acids.Chemical science · 2016Article
- Flexibility Coexists with Shape-Persistence in Cyanostar Macrocycles.Journal of the American Chemical Society · 2016Article
- Visualizing energy landscapes with metric disconnectivity graphs.Journal of computational chemistry · 2014Article
- Molecular dynamics of the proline switch and its role in Crk signaling.The journal of physical chemistry. B · 2014Article
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Authors and funding
2 authors.
Funding
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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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.