Molecular dynamics simulation and experimental study of the surface-display of SPA protein via Lpp-OmpA system for screening of IgG

Vahed, Majid; Ramezani, Fatemeh; Tafakori, Vida; Mirbagheri, V.S.; Najafi, Ali; Ahmadian, Gholamreza

doi:10.1186/s13568-020-01097-1

Cited by 10 publications

(6 citation statements)

References 33 publications

(38 reference statements)

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“…At first, Nf had the excellent dispersion and film forming ability, thus it was used to obtain rGO-PEI-Ag-Nf solution, which was bounded to electrode. After that, the amino group of SPA could be assembled on the electrode surface due to the electrostatic interaction with the silver nanoparticles, and SPA can specifically recognize and bind the Fc part of the antibody by Vander Waals interaction, hydrogen binding and ionic binding [ 42 ]. Finally, using bovine serum albumin (BSA) to block the other unbound active sites, the sensor has been prepared and could be used for the detection of ASA.…”

Section: Resultsmentioning

confidence: 99%

An Electrochemical Immunosensor Based on SPA and rGO-PEI-Ag-Nf for the Detection of Arsanilic Acid

Wang

Zhang

et al. 2021

Molecules

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A sensitive electrochemical immunosensor was prepared for rapid detection of ASA based on arsanilic acid (ASA) monoclonal antibody with high affinity. In the preparation of nanomaterials, polyethyleneimine (PEI) improved the stability of the solution and acted as a reducing agent to generate reduced graphene oxide (rGO) with relatively strong conductivity, thereby promoting the transfer of electrons. The dual conductivity of rGO and silver nanoparticles (AgNPs) improved the sensitivity of the sensor. The synthesis of nanomaterials were confirmed by UV-Vis spectroscopy, X-ray diffraction, transmission electron microscopy and scanning electron microscopy. In the optimal experiment conditions, the sensor could achieve the detection range of 0.50–500 ng mL−1 and the limit of detection (LOD) of 0.38 ng mL−1 (S/N = 3). Moreover, the sensor exhibited excellent specificity and acceptable stability, suggesting that the proposed sensor possessed a good potential in ASA detection. Thus, the as-prepared biosensor may be a potential way for detecting other antibiotics in meat and animal-derived foods.

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Section: Resultsmentioning

confidence: 99%

An Electrochemical Immunosensor Based on SPA and rGO-PEI-Ag-Nf for the Detection of Arsanilic Acid

Wang

Zhang

et al. 2021

Molecules

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“…Regardless of the type of host cells selected for molecular display, the anchoring protein must be valid and effective. For example, OmpA has been investigated and used as an anchoring protein to display a foreign protein on the cell surface of E. coli [ 41 , 42 ]. It is usually used as a lipoprotein, which is fused to residues 46–159 of the OmpA porin protein family to anchor to the E. coli cell wall envelope.…”

Section: Principle Of Molecular Display Technology Using Yeastsmentioning

confidence: 99%

Progress of Molecular Display Technology Using Saccharomyces cerevisiae to Achieve Sustainable Development Goals

Shibasaki

Ueda

2023

Microorganisms

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In the long history of microorganism use, yeasts have been developed as hosts for producing biologically active compounds or for conventional fermentation. Since the introduction of genetic engineering, recombinant proteins have been designed and produced using yeast or bacterial cells. Yeasts have the unique property of expressing genes derived from both prokaryotes and eukaryotes. Saccharomyces cerevisiae is one of the well-studied yeasts in genetic engineering. Recently, molecular display technology, which involves a protein-producing system on the yeast cell surface, has been established. Using this technology, designed proteins can be displayed on the cell surface, and novel abilities are endowed to the host yeast strain. This review summarizes various molecular yeast display technologies and their principles and applications. Moreover, S. cerevisiae laboratory strains generated using molecular display technology for sustainable development are described. Each application of a molecular displayed yeast cell is also associated with the corresponding Sustainable Development Goals of the United Nations.

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“…Then, the PDB file of the protein-graphene complex, which had the lowest binding energy, was used as the MD input file. MD simulations were performed using GROMACS software according to several previous studies [20][21][22][23][24]. All bonded and nonbonded parameters for graphene atoms were entered into the OPLSAA force field.…”

Section: Molecular Dynamicsmentioning

confidence: 99%

Evaluation of the Structure and Conformation of Albumin Protein after Interaction with Graphene and Graphene Oxide

Hossein¹,

Ramezani²

2022

Nano BioMed ENG

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Given the increasing demand for graphene-based nanomaterials, it seems necessary to study their effects on the biomolecules they encounter. In this study, we will present the results of our computational study on the influence of graphene and graphene oxide (GO) on albumin. The interaction between albumin, graphene and GO was investigated using molecular dynamics and GROMACS software for 100 ns with a TIP3P water model. Binding energy, its root-mean-square deviation and structural changes were calculated. The molecular dynamics results show that the interaction of albumin with both graphene and GO structures causes changes in protein structure and that GO has a larger effect on the secondary structure. The results show that the binding energy between albumin and graphene is higher than that of GO. The analysis shows that it is more related to non-polar or hydrophobic interactions in the albumin-graphene interaction. Graphene and GO affect the protein microenvironment and reduce the amount of secondary structure, but in general the degree of change depends on the ratio of graphene or GO to albumin, GO functional groups, temperature and pH.

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Molecular dynamics simulation and experimental study of the surface-display of SPA protein via Lpp-OmpA system for screening of IgG

Cited by 10 publications

References 33 publications

An Electrochemical Immunosensor Based on SPA and rGO-PEI-Ag-Nf for the Detection of Arsanilic Acid

An Electrochemical Immunosensor Based on SPA and rGO-PEI-Ag-Nf for the Detection of Arsanilic Acid

Progress of Molecular Display Technology Using Saccharomyces cerevisiae to Achieve Sustainable Development Goals

Evaluation of the Structure and Conformation of Albumin Protein after Interaction with Graphene and Graphene Oxide

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