Simulation insight into the cytochrome c adsorption on graphene and graphene oxide surfaces

Zhao, Daohui; Li, Libo; Zhou, Jian

doi:10.1016/j.apsusc.2017.09.190

Cited by 43 publications

(38 citation statements)

References 82 publications

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“…The same tendency is seen for laccase deposition via available -OH groups of the laccase enzyme. The increase in covalent energy bonding via TYR molecules can be caused by interactions between delocalized electrons of benzene rings which lead to their parallel arrangement [45]. Energy binding of laccase amino acids is closely related to the energy barrier of covalent bond creation.…”

Section: Energy Bonding Characterization Of Laccase Amino Acids Onto mentioning

confidence: 99%

“…The mechanism of protein interplaying with the solid support has been described using molecular dynamic methods, which can provide information such as orientation, conformational changes or key adsorbing residues. These methods have been applied to understand immobilization mechanism via the adsorption process of cytochrome C onto carboxyl-terminated self-assembled monolayer or graphene oxide [45], myoglobin onto rutile (110) and (001) surfaces [46], ribonuclease A [47], lysozyme [48] as well as laccase [49][50][51]. To date, the mechanism of the immobilization process has not been described by density functional theory (DFT) methods.…”

Section: Introductionmentioning

confidence: 99%

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Theoretical insight into plasma deposition of laccase bio-coating formation

Malinowski

Jaroszyńska-Wolińska

Herbert³

2019

J Mater Sci

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Development of new techniques for deposition of biologically active coatings in the form of bio-recognition layers in biosensor construction is a current technological challenge. Biosensors are widely applied in environmental protection in determination of hazardous materials, e.g., catechol, hydrochinon or resorcinol. Application of a soft plasma polymerization (SPP) technique by lowenergy-density corona discharge has allowed significant simplification of the deposition process of bio-recognition layers. However, the mechanism of the SPP process is by no means fully understood. This paper presents insights into the mechanism of binding laccase enzyme onto graphene oxide (GO) and multiwalled carbon nanotubes (MWCNT) through analysis carried out by density functional theory (DFT) methods and Fourier transform infrared spectroscopy (FTIR). The objective was to examine the mechanism on the basis of binding energies and electrostatic interactions between laccase and carbon nanomaterials as well as enzyme structure after cold plasma deposition. The lowest binding energies have been calculated for the ON bond between the arginine amino acid of laccase and the hydroxyl group of GO and the CO bond between the serine molecule of laccase and the carboxyl groups of GO and MWCNT. FTIR and DFT studies showed that the chemical structures of the laccase enzyme and carbon nanomaterials after corona jet plasma treatment are not substantially changed. Preliminary recognition of the mechanism of biosensing layer deposition by the SPP technique opens the way to application of this innovative technique to the construction of other biosensors such as for determination of pollutants in water samples.

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Section: Energy Bonding Characterization Of Laccase Amino Acids Onto mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Theoretical insight into plasma deposition of laccase bio-coating formation

Malinowski

Jaroszyńska-Wolińska

Herbert³

2019

J Mater Sci

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“…Fig. 1 represents the quantitative characterization 40,41 of the orientation angles and protein proximity concerning the substrate. The end-on A and side-on B congurations had the a-helix at 21Å from the substrate.…”

Section: Methodsmentioning

confidence: 99%

Orientation effects on the nanoscale adsorption behavior of bone morphogenetic protein-2 on hydrophilic silicon dioxide

Marquetti

Desai

2019

RSC Adv.

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“…Moreover, adsorption of cyt c over GO/reduced GO (rGO) resulted in a modulation of the protein activity due to the changes in the heme micro environment caused by the different interactions between the protein and the materials [ 206 ]. Zhao et al [ 207 ] reported the study of cyt c adsorption over graphene and GO by mean of parallel tempered Monte Carlo (PTMC) algorithm coupled with MD simulations to assess the orientation of protein on the surface, the nature of the interactions, the subsequent conformational changes and the ET pathway. With the PTCM method, cyt c is considered in a united-residue model in which each amino acid is reduced to a site centered interaction at the carbon alpha, and the structure of the whole protein is kept rigid.…”

Section: Protein/surface Interactionsmentioning

confidence: 99%

“… The electron transfer pathway of Cyt c on the graphene oxide (GO) surface. Reprinted with permission from [ 207 ]. Copyright (2018) Elsevier.…”

Section: Figurementioning

confidence: 99%

Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?

Osella

2021

Nanomaterials

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A tremendous effort is currently devoted to the generation of novel hybrid materials with enhanced electronic properties for the creation of artificial photosynthetic systems. This compelling and challenging problem is well-defined from an experimental point of view, as the design of such materials relies on combining organic materials or metals with biological systems like light harvesting and redox-active proteins. Such hybrid systems can be used, e.g., as bio-sensors, bio-fuel cells, biohybrid photoelectrochemical cells, and nanostructured photoelectronic devices. Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET). It is within this aspect that computation can make the difference and improve the current understanding of the mechanisms underneath the interface formation and the charge transfer efficiency. Yet, the systems considered (i.e., light harvesting protein, self-assembly monolayer and surface assembly) are more and more complex, reaching (and often passing) the limit of current computation power. In this review, recent developments in computational methods for studying complex interfaces for artificial photosynthesis will be provided and selected cases discussed, to assess the inherent ability of computation to leave a mark in this field of research.

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Simulation insight into the cytochrome c adsorption on graphene and graphene oxide surfaces

Cited by 43 publications

References 82 publications

Theoretical insight into plasma deposition of laccase bio-coating formation

Theoretical insight into plasma deposition of laccase bio-coating formation

Orientation effects on the nanoscale adsorption behavior of bone morphogenetic protein-2 on hydrophilic silicon dioxide

Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?

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