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Title:In silico generation of peptides by replica exchange Monte Carlo: Docking-based optimization of maltose-binding-protein ligands
Authors:Russo, Anna (Author)
Scognamiglio, Pasqualina Liana (Author)
Hong Enriquez, Rolando Pablo (Author)
Santambrogio, Carlo (Author)
Grandori, Rita (Author)
Marasco, Daniela (Author)
Giordano, Antonio (Author)
Scoles, Giacinto (Author)
Fortuna, Sara (Author)
Files:.pdf 11_Russo_MBP.pdf (4,27 MB)
Work type:Not categorized (r6)
Tipology:1.01 - Original Scientific Article
Organization:UNG - University of Nova Gorica
Abstract:Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based algorithms allow for a computational screening of peptides as binders. Here we developed ex-novo peptides targeting the maltose site of the Maltose Binding Protein, the prototypical system for the study of protein ligand recognition. We used a Monte Carlo based protocol, to computationally evolve a set of octapeptides starting from a polialanine sequence. We screened in silico the candidate peptides and characterized their binding abilities by surface plasmon resonance, fluorescence and electrospray ionization mass spectrometry assays. These experiments showed the designed binders to recognize their target with micromolar affinity. We finally discuss the obtained results in the light of further improvement in the ex-novo optimization of peptide based binders.
Keywords:peptides, docking, optimisation, computation, maltose binding protein, probe, ligand
Year of publishing:2015
Number of pages:16
Numbering:8, 10
COBISS_ID:4536059  Link is opened in a new window
DOI:10.1371/journal.pone.0133571 Link is opened in a new window
License:CC BY 4.0
This work is available under this license: Creative Commons Attribution 4.0 International
Categories:Document is not linked to any category.
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Record is a part of a journal

Title:PLoS ONE
Publisher:Public Library of Science
Year of publishing:2015