ArticleProtein science : a publication of the Protein Society2008
Unfolding the fold of cyclic cysteine-rich peptides.
Article in Protein science : a publication of the Protein Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Active Targeting of Cancer Cells by Nanobody Decorated Polypeptide Micelle with Bio-orthogonally Conjugated Drug.Nano letters · 2019Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- The chemistry and biology of theta defensins.Angewandte Chemie (International ed. in English) · 2014Review
- Rapid sampling of local minima in protein energy surface and effective reduction through a multi-objective filter.Proteome science · 2013Article
- Exploring the Energy Landscapes of Cyclic Tetrapeptides with Discrete Path Sampling.Journal of chemical theory and computation · 2013Article
- A population-based evolutionary search approach to the multiple minima problem in de novo protein structure prediction.BMC structural biology · 2013Article
- Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface.Proteome science · 2012Article
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3 authors.
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Abstract
We propose a method to extensively characterize the native state ensemble of cyclic cysteine-rich peptides. The method uses minimal information, namely, amino acid sequence and cyclization, as a topological feature that characterizes the native state. The method does not assume a specific disulfide bond pairing for cysteines and allows the possibility of unpaired cysteines. A detailed view of the conformational space relevant for the native state is obtained through a hierarchic multi-resolution exploration. A crucial feature of the exploration is a geometric approach that efficiently generates a large number of distinct cyclic conformations independently of one another. A spatial and energetic analysis of the generated conformations associates a free-energy landscape to the explored conformational space. Application to three long cyclic peptides of different folds shows that the conformational ensembles and cysteine arrangements associated with free energy minima are fully consistent with available experimental data. The results provide a detailed analysis of the native state features of cyclic peptides that can be further tested in experiment.
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