Evaluation of ochratoxin recognition by peptides using explicit solvent molecular dynamics

Aby A. Thyparambil, Ingrid Bazin, Anthony Guiseppi-Elie

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


Biosensing platforms based on peptide recognition provide a cost-effective and stable alternative to antibody-based capture and discrimination of ochratoxin-A (OTA) vs. ochratoxin-B (OTB) in monitoring bioassays. Attempts to engineer peptides with improved recognition efficacy require thorough structural and thermodynamic characterization of the binding-competent conformations. Classical molecular dynamics (MD) approaches alone do not provide a thorough assessment of a peptide’s recognition efficacy. In this study, in-solution binding properties of four different peptides, a hexamer (SNLHPK), an octamer (CSIVEDGK), NFO4 (VYMNRKYYKCCK), and a 13-mer (GPAGIDGPAGIRC), which were previously generated for OTA-specific recognition, were evaluated using an advanced MD simulation approach involving accelerated configurational search and predictive modeling. Peptide configurations relevant to ochratoxin binding were initially generated using biased exchange metadynamics and the dynamic properties associated with the in-solution peptide–ochratoxin binding were derived from Markov State Models. Among the various peptides, NFO4 shows superior in-solution OTA sensing and also shows superior selectivity for OTA vs. OTB due to the lower penalty associated with solvating its bound complex. Advanced MD approaches provide structural and energetic insights critical to the hapten-specific recognition to aid the engineering of peptides with better sensing efficacies.

Original languageEnglish (US)
Article number164
Issue number5
StatePublished - May 13 2017


  • Biased exchange metadynamics
  • Binding free energy
  • Markov state model
  • Molecular dynamics
  • Mycotoxin recognition
  • NFO4
  • Ochratoxins
  • Peptide
  • Solvation penalty
  • Toxins

ASJC Scopus subject areas

  • Toxicology
  • Health, Toxicology and Mutagenesis


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