Parameterization of an interfacial force field for accurate representation of peptide adsorption free energy on high-density polyethylene

Abramyan, Tigran M.; Snyder, James A.; Yancey, Jeremy A.; Thyparambil, Aby A.; Wei, Yang; Stuart, Steven J.; Latour, Robert A.

doi:10.1116/1.4916361

Cited by 12 publications

(20 citation statements)

References 51 publications

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“…AMP docking computations were performed with the Autodock 4.2 software 30 specifically modified with the help of an artificial intelligence procedure, to cope with nucleic-acid targets 30 . This software modification has already been validated and proven its reliability [31][32][33] . The Lamarckian Genetic Algorithm was employed 34 for the global optimum binding position search.…”

Section: In-silico Constructionsmentioning

confidence: 95%

Computational studies of a DNA-based aptasensor: toward theory-driven transduction improvement.

Araujo-Rocha

Piro

Noël

et al. 2021

Preprint

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Aptamers are a class of bioreceptors intensively used in current analytical tools dedicated to molecular diagnostics due to their ability to perform large structural reorganization upon target binding. However, there is a lack of methodologies allowing to rationalize their structure in order to improve the transduction efficiency in aptamer sensors. We choose here, as a model system, a three-strand DNA structure as probe, composed of two DNA strands anchored on a gold surface and partially hybridized with an aptamer sequence sensitive to Ampicillin (AMP). The DNA structure has been designed to show strong structural change upon AMP binding to its aptamer.Using a set of computational techniques including molecular dynamics simulations, we deeply investigated the structure change upon analyte binding, taking into account the grafting on the surface. Original analyses of ions distributions along the trajectories unveil a distinct pattern between both states which can be related to changes in capacitance of the interface between these states. To our knowledge, this work demonstrates for the first time the ability of computational investigations to drive, in-silico, the design of aptasensors.

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Section: In-silico Constructionsmentioning

confidence: 95%

Computational studies of a DNA-based aptasensor: toward theory-driven transduction improvement.

Araujo-Rocha

Piro

Noël

et al. 2021

Preprint

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“…The foregoing requires that a clear energetic distinction be established between bound and unbound states, for which energetically accessible receptor and mycotoxin conformations should be calculated. For such type of molecular estimations and visualization, all-atom MD simulations are appropriate and quite frequently used [ 28 , 29 , 112 , 113 , 114 , 115 ].…”

Section: Molecular Modeling Approaches Towards Design and Fabricatmentioning

confidence: 99%

“…Many groups have since developed a separate set of force field parameters to describe the behavior of the peptide at the solid-liquid interface [ 54 , 117 , 118 ]. Such parameters are currently available for a few model surfaces such as crystalline glass, high-density polyethylene, and graphene [ 99 , 114 , 115 ]. However, the interfacial force field parameters are limited to a few materials and need to be optimized for every newer generations of force fields.…”

Section: Molecular Modeling Approaches Towards Design and Fabricatmentioning

confidence: 99%

Molecular Modeling and Simulation Tools in the Development of Peptide-Based Biosensors for Mycotoxin Detection: Example of Ochratoxin

Thyparambil

Bazin

Guiseppi‐Elie

2017

Toxins

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Mycotoxin contamination of food and feed is now ubiquitous. Exposures to mycotoxin via contact or ingestion can potentially induce adverse health outcomes. Affordable mycotoxin-monitoring systems are highly desired but are limited by (a) the reliance on technically challenging and costly molecular recognition by immuno-capture technologies; and (b) the lack of predictive tools for directing the optimization of alternative molecular recognition modalities. Our group has been exploring the development of ochratoxin detection and monitoring systems using the peptide NFO4 as the molecular recognition receptor in fluorescence, electrochemical and multimodal biosensors. Using ochratoxin as the model mycotoxin, we share our perspective on addressing the technical challenges involved in biosensor fabrication, namely: (a) peptide receptor design; and (b) performance evaluation. Subsequently, the scope and utility of molecular modeling and simulation (MMS) approaches to address the above challenges are described. Informed and enabled by phage display, the subsequent application of MMS approaches can rationally guide subsequent biomolecular engineering of peptide receptors, including bioconjugation and bioimmobilization approaches to be used in the fabrication of peptide biosensors. MMS approaches thus have the potential to reduce biosensor development cost, extend product life cycle, and facilitate multi-analyte detection of mycotoxins, each of which positively contributes to the overall affordability of mycotoxin biosensor monitoring systems.

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“…This method successfully reproduced the free energy of adsorption on hydrophobic SAMs without affecting the same measure over hydrophilic SAMs. The Dual-FF approach has also been applied to silica [57] and high-density polyethylene [58] to reproduce experimental adsorption data. While this solution achieves the goal of reproducing the desired experimental data, it is a practical solution, which neglects the possibility of underlying errors in the parametrization of the surface.…”

Section: Interfacial Force Fields and Surface Modelsmentioning

confidence: 99%

“…The model reflected the trends from experiment, but the parameters were not optimized for polypropylene so absolute values could not be compared. Most recently, the dual-FF philosophy for CHARMM originally developed for SAMs was applied to high-density polyethylene [58]. Surface characterization included atomic composition and water contact angle, but these were not used for optimization of the surface parameters.…”

Section: Experimental Target Data and Validation Datamentioning

confidence: 99%

Force fields for simulating the interaction of surfaces with biological molecules

et al. 2016

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The interaction of biomolecules with solid interfaces is of fundamental importance to several emerging biotechnologies such as medical implants, anti-fouling coatings and novel diagnostic devices. Many of these technologies rely on the binding of peptides to a solid surface, but a full understanding of the mechanism of binding, as well as the effect on the conformation of adsorbed peptides, is beyond the resolution of current experimental techniques. Nanoscale simulations using molecular mechanics offer potential insights into these processes. However, most models at this scale have been developed for aqueous peptide and protein simulation, and there are no proven models for describing biointerfaces. In this review, we detail the current research towards developing a non-polarizable molecular model for peptide-surface interactions, with a particular focus on fitting the model parameters as well as validation by choice of appropriate experimental data.

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Parameterization of an interfacial force field for accurate representation of peptide adsorption free energy on high-density polyethylene

Cited by 12 publications

References 51 publications

Computational studies of a DNA-based aptasensor: toward theory-driven transduction improvement.

Computational studies of a DNA-based aptasensor: toward theory-driven transduction improvement.

Molecular Modeling and Simulation Tools in the Development of Peptide-Based Biosensors for Mycotoxin Detection: Example of Ochratoxin

Force fields for simulating the interaction of surfaces with biological molecules

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