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EnglishShort peptides offer a cheap alternative to antibodies for developing sensing units in devices for concentration measurement. We here describe a computational procedure that allows designing peptides capable of binding with high affinity a target organic molecule in aqueous or nonstandard solvent environments. The algorithm is based on a stochastic search in the space of the possible sequences of the peptide, and exploits finite temperature molecular dynamics simulations in explicit solvent to check if a proposed mutation improves the binding affinity or not. The procedure automatically produces peptides which form thermally stable complexes with the target. The estimated binding free energy reaches the 13 kcal/mol for Irinotecan anticancer drug, the target considered in this work. These peptides are by construction solvent specific; namely, they recognize the target only in the solvent in which they have been designed. This feature of the algorithm calls for applications in devices in which the peptide-based sensor is required to work in denaturants or under extreme conditions of pressure and temperature.
| Titolo: | Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics |
| Autori: | |
| Data di pubblicazione: | 2015 |
| Rivista: | |
| Abstract: | Short peptides offer a cheap alternative to antibodies for developing sensing units in devices for concentration measurement. We here describe a computational procedure that allows designing peptides capable of binding with high affinity a target organic molecule in aqueous or nonstandard solvent environments. The algorithm is based on a stochastic search in the space of the possible sequences of the peptide, and exploits finite temperature molecular dynamics simulations in explicit solvent to check if a proposed mutation improves the binding affinity or not. The procedure automatically produces peptides which form thermally stable complexes with the target. The estimated binding free energy reaches the 13 kcal/mol for Irinotecan anticancer drug, the target considered in this work. These peptides are by construction solvent specific; namely, they recognize the target only in the solvent in which they have been designed. This feature of the algorithm calls for applications in devices in which the peptide-based sensor is required to work in denaturants or under extreme conditions of pressure and temperature. |
| Handle: | http://hdl.handle.net/11368/2848524 |
| Digital Object Identifier (DOI): | http://dx.doi.org/10.1021/acs.jpcb.5b06227 |
| URL: | http://pubs.acs.org/journal/jpcbfk |
| Appare nelle tipologie: | 1.1 Articolo in Rivista |
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| File | Descrizione | Tipologia | Licenza | |
|---|---|---|---|---|
| Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics.pdf | pdf editoriale | Documento in Versione Editoriale | Digital Rights Management non definito | Administrator Richiedi una copia |
| proof-2.pdf | Bozza finale post-referaggio (post-print) |  | Open Access Visualizza/Apri |
