[en] We extended the use of Peplook, an in silico procedure for the prediction of three-dimensional (3D) models of linear peptides to the prediction of 3D models of cyclic peptides and thanks to the ab initio calculation procedure, to the calculation of peptides with non-proteinogenic amino acids. Indeed, such peptides cannot be predicted by homology or threading. We compare the calculated models with NMR and X-ray models and for the cyclic peptides, with models predicted by other in silico procedures (Pep-Fold and I-Tasser). For cyclic peptides, on a set of 38 peptides, average root mean square deviation of backbone atoms (BB-RMSD) was 3.8 and 4.1 A for Peplook and Pep-Fold, respectively. The best results are obtained with I-Tasser (2.5 A) although evaluations were biased by the fact that the resolved Protein Data Bank models could be used as template by the server. Peplook and Pep-Fold give similar results, better for short (up to 20 residues) than for longer peptides. For peptides with non-proteinogenic residues, performances of Peplook are sound with an average BB-RMSD of 3.6 A for 'non-natural peptides' and 3.4 A for peptides combining non-proteinogenic residues and cyclic structure. These results open interesting possibilities for the design of peptidic drugs. Copyright (c) 2011 European Peptide Society and John Wiley & Sons, Ltd.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Beaufays, Jérôme ✱; Université de Liège - ULiège > Chimie et bio-industries > Centre de Bio. Fond. - Section de Biophysique moléc. numér.
Lins, Laurence ✱; Université de Liège - ULiège > Chimie et bio-industries > Centre de Bio. Fond. - Section de Biophysique moléc. numér.
Thomas, Annick ; Université de Liège - ULiège > Chimie et bio-industries > Centre de Bio. Fond. - Section de Biophysique moléc. numér.
Brasseur, Robert ; Université de Liège - ULiège > Chimie et bio-industries > Centre de Bio. Fond. - Section de Biophysique moléc. numér.
✱ These authors have contributed equally to this work.
Language :
English
Title :
In silico predictions of 3D structures of linear and cyclic peptides with natural and non-proteinogenic residues.
Publication date :
2012
Journal title :
Journal of Peptide Science
ISSN :
1075-2617
eISSN :
1099-1387
Publisher :
John Wiley & Sons, Inc, Chichester, United Kingdom
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