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Unfolding the fold of cyclic cysteine-rich peptides.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Clementi, Cecilia Shehu, Amarda Kavraki, Lydia E.
Description	Country affiliation: United States Author Affiliation: Shehu A ( Department of Computer Science, Rice University, Houston, Texas 77005, USA.)
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.
ISSN	09618368
e-ISSN	1469896X
DOI	10.1110/ps.073142708
Journal	Protein Science
Issue Number	3
Volume Number	17
Language	English
Publisher	Wiley-Blackwell (on behalf of The Protein Society)
Publisher Date	2008-03-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Computational Biology Cysteine Chemistry Peptides, Cyclic Animals Conotoxins Cyclotides Defensins Macaca Mulatta Models, Molecular Nuclear Magnetic Resonance, Biomolecular Protein Folding Protein Structure, Secondary Sequence Analysis, Protein Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s. Discipline Biochemistry
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Biochemistry

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