Evaluation of Ochratoxin Recognition by Peptides Using Explicit Solvent Molecular Dynamics

Toxins
Aby A ThyparambilAnthony Guiseppi-Elie

Abstract

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 penal...Continue Reading

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Citations

Jul 29, 2017·Journal of Chemical Information and Modeling·Aby A ThyparambilAnthony Guiseppi-Elie
Nov 3, 2020·Biotechnology and Bioengineering·Zahra KhoshbinAsma Verdian
Dec 2, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Luna Rodriguez-SalazarAndrés Cifuentes

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Methods Mentioned

BETA
enzyme-linked immunosorbent assays
phage display
surface plasmon resonance
Biosensing
peptide folding

Software Mentioned

REMD
mmpbsa
DSSP
pyEMMA
Visual Molecular Dynamics ( VMD
Visual Molecular Dynamics
PLUMED
GROMACS
GROMOS
MDtraj

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