In-silico design of peptide receptor for carboxyhemoglobin recognition

Rodriguez-Salazar, Luna; Guevara-Pulido, James; Esteban, Morales-Mendoza; Francisco, Ibla

doi:10.1016/j.imu.2019.01.003

Cited by 3 publications

(10 citation statements)

References 20 publications

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“…Therefore, for the bioreceptor 2.1, the possible interactions that existed before adding the methylene bridges were lost. This result contradicts that of a previous study [ 18 ], but if it is considered that the substrate size in the study was much larger compared to DA, it could be deduced that DA can only generate a few interactions.…”

Section: Resultscontrasting

confidence: 99%

“…As expected, the results indicated that the affinity of the three bioreceptors for DA was lower than the affinity of DAT for DA, which is −5.2 kcal/mol. As previously reported, these results were expected because the steric hindrance exhibited by a peptide within this design length range is not comparable with that of a target [18].…”

Section: Bioreceptor Codesupporting

confidence: 61%

“…Thus, two options were considered. The first was to consider the number of residues between the selected amino acids from each hot spot, and the second was to increase the steric volume of the bioreceptors in order to increase their affinity [ 18 ].…”

Section: Resultsmentioning

confidence: 99%

“…For example, peptides are emerging as an alternative for molecular recognition, as they are considered versatile molecules because they can be synthesized with a wide variety of structural modifications [ 16 , 17 ]. In silico models of peptide bioreceptors [ 18 ] and peptide-based biosensors have already been designed for substrate recognition [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, our in silico study focuses on designing bioreceptors capable of recognizing a particular substrate [ 18 ], in this case DA, as a previous step to synthesizing the most promising bioreceptors obtained. This way, the in vitro design and testing process can be more efficient and faster due to the implementation of bioinformatics tools, such as molecular modeling, to assess and improve the bioreceptor–ligand interaction compared to that of the protein–ligand complex interaction [ 20 ] between DA and the DA transporter (DAT) during dopaminergic neurotransmission [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

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In Silico Design of a Peptide Receptor for Dopamine Recognition

2020

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Dopamine (DA) is an important neurotransmitter with a fundamental role in regulatory functions related to the central, peripheral, renal, and hormonal nervous systems. Dopaminergic neurotransmission dysfunctions are commonly associated with several diseases; thus, in situ quantification of DA is a major challenge. To achieve this goal, enzyme-based biosensors have been employed for substrate recognition in the past. However, due to their sensitivity to changes in temperature and pH levels, new peptide bioreceptors have been developed. Therefore, in this study, four bioreceptors were designed in silico to exhibit a higher affinity for DA than the DA transporters (DATs). The design was based on the hot spots of the active sites of crystallized enzyme structures that are physiologically related to DA. The affinities between the chosen targets and designed bioreceptors were calculated using AutoDock Vina. Additionally, the binding free energy, ∆G, of the dopamine-4xp1 complex was calculated by molecular dynamics (MD). This value presented a direct relationship with the E_refine value obtained from molecular docking based on the ∆G functions obtained from MOE of the promising bioreceptors. The control variables in the design were amino acids, bond type, steric volume, stereochemistry, affinity, and interaction distances. As part of the results, three out of the four bioreceptor candidates presented promising values in terms of DA affinity and distance.

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Section: Resultscontrasting

confidence: 99%

Section: Bioreceptor Codesupporting

confidence: 61%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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In Silico Design of a Peptide Receptor for Dopamine Recognition

2020

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Computational Studies of a DNA-Based Aptasensor: toward Theory-Driven Transduction Improvement

et al. 2021

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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 us 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 the 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 ion 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 the ability of computational investigations for the first time to drive, in silico, the design of aptasensors.

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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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In-silico design of peptide receptor for carboxyhemoglobin recognition

Cited by 3 publications

References 20 publications

In Silico Design of a Peptide Receptor for Dopamine Recognition

In Silico Design of a Peptide Receptor for Dopamine Recognition

Computational Studies of a DNA-Based Aptasensor: toward Theory-Driven Transduction Improvement

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

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